├── .gitignore ├── LICENSE ├── README.md ├── data ├── Source Data.zip ├── sampledata.bed ├── sampledata.bedpe ├── sampledata.csv └── sampledata2.csv ├── phenosv.yml ├── phenosv ├── Phen2Gene │ ├── __init__.py │ ├── calculation.py │ ├── filter.py │ ├── json_format.py │ ├── outdated_HP │ │ ├── HP_0000057 │ │ ├── HP_0000284 │ │ ├── HP_0000361 │ │ ├── HP_0000487 │ │ ├── HP_0000489 │ │ ├── HP_0000547 │ │ ├── HP_0000611 │ │ ├── HP_0000655 │ │ ├── HP_0000833 │ │ ├── HP_0001002 │ │ ├── HP_0001011 │ │ ├── HP_0001113 │ │ ├── HP_0001122 │ │ ├── HP_0001145 │ │ ├── HP_0001146 │ │ ├── HP_0001150 │ │ ├── HP_0001226 │ │ ├── HP_0001322 │ │ ├── HP_0001379 │ │ ├── HP_0001380 │ │ ├── HP_0001400 │ │ ├── HP_0001472 │ │ ├── HP_0001487 │ │ ├── HP_0001587 │ │ ├── HP_0001606 │ │ ├── HP_0001613 │ │ ├── HP_0001673 │ │ ├── HP_0001675 │ │ ├── HP_0001676 │ │ ├── HP_0001724 │ │ ├── HP_0001726 │ │ ├── HP_0001862 │ │ ├── HP_0002109 │ │ ├── HP_0002271 │ │ ├── HP_0002281 │ │ ├── HP_0002377 │ │ ├── HP_0002459 │ │ ├── HP_0002564 │ │ ├── HP_0002622 │ │ ├── HP_0002631 │ │ ├── HP_0002755 │ │ ├── HP_0002773 │ │ ├── HP_0002845 │ │ ├── HP_0002880 │ │ ├── HP_0002924 │ │ ├── HP_0003114 │ │ ├── HP_0003295 │ │ ├── HP_0003335 │ │ ├── HP_0003340 │ │ ├── HP_0003421 │ │ ├── HP_0003464 │ │ ├── HP_0003490 │ │ ├── HP_0003494 │ │ ├── HP_0003553 │ │ ├── HP_0003975 │ │ ├── HP_0004066 │ │ ├── HP_0004083 │ │ ├── HP_0004090 │ │ ├── HP_0004110 │ │ ├── HP_0004121 │ │ ├── HP_0004138 │ │ ├── HP_0004139 │ │ ├── HP_0004143 │ │ ├── HP_0004144 │ │ ├── HP_0004153 │ │ ├── HP_0004157 │ │ ├── HP_0004161 │ │ ├── HP_0004162 │ │ ├── HP_0004168 │ │ ├── HP_0004174 │ │ ├── HP_0004175 │ │ ├── HP_0004183 │ │ ├── HP_0004184 │ │ ├── HP_0004185 │ │ ├── HP_0004186 │ │ ├── HP_0004187 │ │ ├── HP_0004192 │ │ ├── HP_0004193 │ │ ├── HP_0004194 │ │ ├── HP_0004196 │ │ ├── HP_0004198 │ │ ├── HP_0004201 │ │ ├── HP_0004202 │ │ ├── HP_0004203 │ │ ├── HP_0004355 │ │ ├── HP_0004367 │ │ ├── HP_0004759 │ │ ├── HP_0004760 │ │ ├── HP_0004928 │ │ ├── HP_0004929 │ │ ├── HP_0004953 │ │ ├── HP_0004954 │ │ ├── HP_0004986 │ │ ├── HP_0005111 │ │ ├── HP_0005114 │ │ ├── HP_0005130 │ │ ├── HP_0005141 │ │ ├── HP_0005173 │ │ ├── HP_0005296 │ │ ├── HP_0005298 │ │ ├── HP_0005299 │ │ ├── HP_0005309 │ │ ├── HP_0005315 │ │ ├── HP_0005364 │ │ ├── HP_0005375 │ │ ├── HP_0005379 │ │ ├── HP_0005397 │ │ ├── HP_0005402 │ │ ├── HP_0005409 │ │ ├── HP_0005549 │ │ ├── HP_0005744 │ │ ├── HP_0005794 │ │ ├── HP_0005833 │ │ ├── HP_0005834 │ │ ├── HP_0005837 │ │ ├── HP_0005901 │ │ ├── HP_0005921 │ │ ├── HP_0006158 │ │ ├── HP_0006525 │ │ ├── HP_0006830 │ │ ├── HP_0006877 │ │ ├── HP_0007087 │ │ ├── HP_0007163 │ │ ├── HP_0007314 │ │ ├── HP_0007316 │ │ ├── HP_0007409 │ │ ├── HP_0007654 │ │ ├── HP_0007659 │ │ ├── HP_0007691 │ │ ├── HP_0007692 │ │ ├── HP_0007698 │ │ ├── HP_0007702 │ │ ├── HP_0007712 │ │ ├── HP_0007713 │ │ ├── HP_0007736 │ │ ├── HP_0007739 │ │ ├── HP_0007744 │ │ ├── HP_0007748 │ │ ├── HP_0007756 │ │ ├── HP_0007757 │ │ ├── HP_0007758 │ │ ├── HP_0007782 │ │ ├── HP_0007783 │ │ ├── HP_0007786 │ │ ├── HP_0007798 │ │ ├── HP_0007801 │ │ ├── HP_0007808 │ │ ├── HP_0007810 │ │ ├── HP_0007825 │ │ ├── HP_0007829 │ │ ├── HP_0007851 │ │ ├── HP_0007852 │ │ ├── HP_0007868 │ │ ├── HP_0007869 │ │ ├── HP_0007876 │ │ ├── HP_0007893 │ │ ├── HP_0007901 │ │ ├── HP_0007910 │ │ ├── HP_0007916 │ │ ├── HP_0007920 │ │ ├── HP_0007923 │ │ ├── HP_0007930 │ │ ├── HP_0007945 │ │ ├── HP_0007949 │ │ ├── HP_0007956 │ │ ├── HP_0007961 │ │ ├── HP_0007981 │ │ ├── HP_0007982 │ │ ├── HP_0008008 │ │ ├── HP_0008012 │ │ ├── HP_0008017 │ │ ├── HP_0008024 │ │ ├── HP_0008033 │ │ ├── HP_0008036 │ │ ├── HP_0008051 │ │ ├── HP_0008230 │ │ ├── HP_0008356 │ │ ├── HP_0008694 │ │ ├── HP_0009044 │ │ ├── HP_0009090 │ │ ├── HP_0009163 │ │ ├── HP_0009448 │ │ ├── HP_0009449 │ │ ├── HP_0009620 │ │ ├── HP_0009621 │ │ ├── HP_0009885 │ │ ├── HP_0010700 │ │ ├── HP_0010905 │ │ ├── HP_0010928 │ │ ├── HP_0011146 │ │ ├── HP_0011148 │ │ ├── HP_0011498 │ │ ├── HP_0011606 │ │ ├── HP_0011607 │ │ ├── HP_0011765 │ │ ├── HP_0012140 │ │ ├── HP_0012201 │ │ ├── HP_0012291 │ │ ├── HP_0012374 │ │ ├── HP_0012455 │ │ ├── HP_0025462 │ │ ├── HP_0025541 │ │ ├── HP_0030013 │ │ ├── HP_0030073 │ │ ├── HP_0030152 │ │ ├── HP_0030332 │ │ ├── HP_0030340 │ │ ├── HP_0030422 │ │ ├── HP_0030523 │ │ ├── HP_0030524 │ │ ├── HP_0030761 │ │ ├── HP_0030960 │ │ ├── HP_0030963 │ │ ├── HP_0030971 │ │ ├── HP_0031440 │ │ ├── HP_0031477 │ │ ├── HP_0031988 │ │ ├── HP_0040037 │ │ ├── HP_0040038 │ │ ├── HP_0040077 │ │ ├── HP_0040193 │ │ ├── HP_0040199 │ │ ├── HP_0040316 │ │ ├── HP_0045013 │ │ ├── HP_0045016 │ │ ├── HP_0045083 │ │ ├── HP_0100609 │ │ ├── HP_0100637 │ │ ├── HP_0100805 │ │ ├── HP_0100843 │ │ ├── HP_0200099 │ │ ├── HP_0200126 │ │ ├── HP_0200129 │ │ ├── HP_0200135 │ │ ├── HP_0200144 │ │ ├── HP_0410004 │ │ ├── HP_0500010 │ │ ├── HP_0500014 │ │ ├── HP_3000001 │ │ └── HP_3000026 │ ├── output.py │ ├── phen2gene.py │ ├── prioritize.py │ ├── score_merge.py │ └── weight_assignment.py ├── __init__.py ├── model │ ├── __init__.py │ ├── annotation.py │ ├── annotation.sh │ ├── data_loader.py │ ├── feature_interpretation.py │ ├── model.py │ ├── model_blocks.py │ ├── operation_function.py │ ├── permutation.py │ ├── phenosv.py │ ├── phenosv.sh │ ├── phenosv_light.sh │ ├── prioritization.py │ ├── test.py │ └── train.py ├── setup.py └── utilities │ ├── __init__.py │ ├── read_features.py │ └── utility.py ├── setup.py ├── setup.sh └── update_config.sh /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/WGLab/PhenoSV/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/WGLab/PhenoSV/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/WGLab/PhenoSV/HEAD/README.md -------------------------------------------------------------------------------- /data/Source Data.zip: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/WGLab/PhenoSV/HEAD/data/Source Data.zip -------------------------------------------------------------------------------- /data/sampledata.bed: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/WGLab/PhenoSV/HEAD/data/sampledata.bed -------------------------------------------------------------------------------- /data/sampledata.bedpe: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/WGLab/PhenoSV/HEAD/data/sampledata.bedpe -------------------------------------------------------------------------------- /data/sampledata.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/WGLab/PhenoSV/HEAD/data/sampledata.csv -------------------------------------------------------------------------------- /data/sampledata2.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/WGLab/PhenoSV/HEAD/data/sampledata2.csv -------------------------------------------------------------------------------- /phenosv.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/WGLab/PhenoSV/HEAD/phenosv.yml -------------------------------------------------------------------------------- /phenosv/Phen2Gene/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/calculation.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/WGLab/PhenoSV/HEAD/phenosv/Phen2Gene/calculation.py -------------------------------------------------------------------------------- /phenosv/Phen2Gene/filter.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/WGLab/PhenoSV/HEAD/phenosv/Phen2Gene/filter.py -------------------------------------------------------------------------------- /phenosv/Phen2Gene/json_format.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/WGLab/PhenoSV/HEAD/phenosv/Phen2Gene/json_format.py -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0000057: -------------------------------------------------------------------------------- 1 | obsolete Clitoromegaly 2 | HP_0008665 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0000284: -------------------------------------------------------------------------------- 1 | obsolete Abnormality of the ocular region 2 | HP_0000315 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0000361: -------------------------------------------------------------------------------- 1 | obsolete Pulsatile tinnitus (tympanic paraganglioma) 2 | HP_0008629 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0000487: -------------------------------------------------------------------------------- 1 | obsolete Congenital strabismus 2 | HP_0000486 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0000489: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/WGLab/PhenoSV/HEAD/phenosv/Phen2Gene/outdated_HP/HP_0000489 -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0000547: -------------------------------------------------------------------------------- 1 | obsolete Tapetoretinal degeneration 2 | HP_0000510 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0000611: -------------------------------------------------------------------------------- 1 | obsolete Choroid coloboma 2 | HP_0000567 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0000655: -------------------------------------------------------------------------------- 1 | obsolete Vitreoretinal degeneration 2 | HP_0007773 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0000833: -------------------------------------------------------------------------------- 1 | obsolete Glucose intolerance 2 | HP_0001952 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0001002: -------------------------------------------------------------------------------- 1 | obsolete Decreased subcutaneous fat 2 | HP_0003758 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0001011: -------------------------------------------------------------------------------- 1 | obsolete Diaphoresis (with pheochromocytoma) 2 | HP_0000975 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0001113: -------------------------------------------------------------------------------- 1 | obsolete Early cataracts 2 | HP_0000518 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0001122: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/WGLab/PhenoSV/HEAD/phenosv/Phen2Gene/outdated_HP/HP_0001122 -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0001145: -------------------------------------------------------------------------------- 1 | obsolete Chorioretinopathy 2 | 3 | HP_0000532 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0001146: -------------------------------------------------------------------------------- 1 | obsolete Pigmentary retinal degeneration 2 | HP_0000580 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0001150: -------------------------------------------------------------------------------- 1 | obsolete Choroidal sclerosis 2 | 3 | HP_0000532 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0001226: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/WGLab/PhenoSV/HEAD/phenosv/Phen2Gene/outdated_HP/HP_0001226 -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0001322: -------------------------------------------------------------------------------- 1 | obsolete Brain very small 2 | HP_0006872 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0001379: -------------------------------------------------------------------------------- 1 | obsolete Degenerative joint disease 2 | HP_0002758 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0001380: -------------------------------------------------------------------------------- 1 | obsolete Ligamentous laxity 2 | HP_0001388 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0001400: -------------------------------------------------------------------------------- 1 | obsolete Hepatic abscesses due to immunodeficiency 2 | HP_0100523 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0001472: -------------------------------------------------------------------------------- 1 | obsolete Familial predisposition 2 | HP_0001426 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0001487: -------------------------------------------------------------------------------- 1 | obsolete Hypopigmented fundi 2 | HP_0007894 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0001587: -------------------------------------------------------------------------------- 1 | obsolete Primary ovarian failure 2 | 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0001606: -------------------------------------------------------------------------------- 1 | obsolete Vocal cord paralysis (caused by tumor impingement) 2 | HP_0001605 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0001613: -------------------------------------------------------------------------------- 1 | obsolete Hoarse voice (caused by tumor impingement) 2 | HP_0001609 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0001673: -------------------------------------------------------------------------------- 1 | obsolete Tachycardia (with pheochromocytoma) 2 | HP_0001649 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0001675: -------------------------------------------------------------------------------- 1 | obsolete Rhythm disturbances associated with pheochromocytoma 2 | HP_0011675 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0001676: -------------------------------------------------------------------------------- 1 | obsolete Palpitations (with pheochromocytoma) 2 | HP_0001962 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0001724: -------------------------------------------------------------------------------- 1 | obsolete Aortic dilatation 2 | HP_0004942 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0001726: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/WGLab/PhenoSV/HEAD/phenosv/Phen2Gene/outdated_HP/HP_0001726 -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0001862: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/WGLab/PhenoSV/HEAD/phenosv/Phen2Gene/outdated_HP/HP_0001862 -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0002109: -------------------------------------------------------------------------------- 1 | obsolete Abnormality of the bronchi 2 | HP_0025426 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0002271: -------------------------------------------------------------------------------- 1 | obsolete Autonomic dysregulation 2 | HP_0012332 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0002281: -------------------------------------------------------------------------------- 1 | obsolete Gray matter heterotopias 2 | HP_0002282 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0002377: -------------------------------------------------------------------------------- 1 | obsolete Paraganglioma-related cranial nerve palsy 2 | HP_0006824 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0002459: -------------------------------------------------------------------------------- 1 | obsolete Dysautonomia 2 | HP_0012332 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0002564: -------------------------------------------------------------------------------- 1 | obsolete Malformation of the heart and great vessels 2 | HP_0030680 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0002622: -------------------------------------------------------------------------------- 1 | obsolete Dissecting aortic dilatation 2 | HP_0002647 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0002631: -------------------------------------------------------------------------------- 1 | obsolete Dilatation of ascending aorta 2 | HP_0002616 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0002755: -------------------------------------------------------------------------------- 1 | obsolete Osteomyelitis due to immunodeficiency 2 | HP_0002754 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0002773: -------------------------------------------------------------------------------- 1 | obsolete Small vertebral bodies 2 | HP_0008479 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0002845: -------------------------------------------------------------------------------- 1 | obsolete Increased proportion of peripheral CD3+ T cells 2 | HP_0002851 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0002880: -------------------------------------------------------------------------------- 1 | obsolete Respiratory difficulties 2 | HP_0002098 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0002924: -------------------------------------------------------------------------------- 1 | obsolete Decreased circulating aldosterone level 2 | HP_0004319 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0003114: -------------------------------------------------------------------------------- 1 | obsolete Abnormal cardiological findings 2 | HP_0001626 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0003295: -------------------------------------------------------------------------------- 1 | obsolete Impaired FSH and LH secretion 2 | 3 | HP_0030339 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0003335: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/WGLab/PhenoSV/HEAD/phenosv/Phen2Gene/outdated_HP/HP_0003335 -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0003340: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/WGLab/PhenoSV/HEAD/phenosv/Phen2Gene/outdated_HP/HP_0003340 -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0003421: -------------------------------------------------------------------------------- 1 | obsolete Platyspondyly (childhood) 2 | HP_0000926 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0003464: -------------------------------------------------------------------------------- 1 | obsolete Abnormal cholesterol homeostasis 2 | HP_0003107 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0003490: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/WGLab/PhenoSV/HEAD/phenosv/Phen2Gene/outdated_HP/HP_0003490 -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0003494: -------------------------------------------------------------------------------- 1 | obsolete Loss of heterozygosity, multiple chromosomes 2 | 3 | HP_0001428 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0003553: -------------------------------------------------------------------------------- 1 | obsolete Cellulitis due to immunodeficiency 2 | HP_0100658 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0003975: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/WGLab/PhenoSV/HEAD/phenosv/Phen2Gene/outdated_HP/HP_0003975 -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0004066: -------------------------------------------------------------------------------- 1 | obsolete Laterally deviated thumb phalanges 2 | 3 | HP_0009602 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0004083: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/WGLab/PhenoSV/HEAD/phenosv/Phen2Gene/outdated_HP/HP_0004083 -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0004090: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/WGLab/PhenoSV/HEAD/phenosv/Phen2Gene/outdated_HP/HP_0004090 -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0004110: -------------------------------------------------------------------------------- 1 | obsolete Radially deviated index finger phalanges 2 | 3 | HP_0009542 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0004121: -------------------------------------------------------------------------------- 1 | obsolete Radially displaced proximal index finger phalanx 2 | 3 | HP_0009544 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0004138: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/WGLab/PhenoSV/HEAD/phenosv/Phen2Gene/outdated_HP/HP_0004138 -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0004139: -------------------------------------------------------------------------------- 1 | obsolete Flared metaphysis of middle phalanx of index finger 2 | 3 | HP_0009569 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0004143: -------------------------------------------------------------------------------- 1 | obsolete Radially deviated terminal index finger phalanx 2 | 3 | HP_0009542 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0004144: -------------------------------------------------------------------------------- 1 | obsolete Duplication of terminal index finger phalanx 2 | HP_0009948 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0004153: -------------------------------------------------------------------------------- 1 | obsolete Overgrowth of middle finger 2 | 3 | HP_0009316 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0004157: -------------------------------------------------------------------------------- 1 | obsolete Accessory middle-finger phalanges 2 | HP_0009963 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0004161: -------------------------------------------------------------------------------- 1 | obsolete Periosteal new bone of middle finger phalanges 2 | 3 | HP_0009316 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0004162: -------------------------------------------------------------------------------- 1 | obsolete Radially pointed middle finger phalanges 2 | 3 | HP_0009316 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0004168: -------------------------------------------------------------------------------- 1 | obsolete Radially pointed proximal middle-finger phalanx 2 | 3 | HP_0009316 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0004174: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/WGLab/PhenoSV/HEAD/phenosv/Phen2Gene/outdated_HP/HP_0004174 -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0004175: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/WGLab/PhenoSV/HEAD/phenosv/Phen2Gene/outdated_HP/HP_0004175 -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0004183: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/WGLab/PhenoSV/HEAD/phenosv/Phen2Gene/outdated_HP/HP_0004183 -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0004184: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/WGLab/PhenoSV/HEAD/phenosv/Phen2Gene/outdated_HP/HP_0004184 -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0004185: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/WGLab/PhenoSV/HEAD/phenosv/Phen2Gene/outdated_HP/HP_0004185 -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0004186: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/WGLab/PhenoSV/HEAD/phenosv/Phen2Gene/outdated_HP/HP_0004186 -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0004187: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/WGLab/PhenoSV/HEAD/phenosv/Phen2Gene/outdated_HP/HP_0004187 -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0004192: -------------------------------------------------------------------------------- 1 | obsolete Bracket epiphyses of the 4th finger 2 | HP_0009394 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0004193: -------------------------------------------------------------------------------- 1 | obsolete Expanded phalanges of the ring finger 2 | 3 | HP_0009172 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0004194: -------------------------------------------------------------------------------- 1 | obsolete Hypoplastic phalanges of the ring finger 2 | 3 | HP_0009408 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0004196: -------------------------------------------------------------------------------- 1 | obsolete Short phalanges of the ring finger 2 | 3 | HP_0009408 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0004198: -------------------------------------------------------------------------------- 1 | obsolete Wide/broad phalanges of the ring finger 2 | 3 | HP_0009172 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0004201: -------------------------------------------------------------------------------- 1 | obsolete Expanded proximal phalanx of the ring finger 2 | HP_0009310 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0004202: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/WGLab/PhenoSV/HEAD/phenosv/Phen2Gene/outdated_HP/HP_0004202 -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0004203: -------------------------------------------------------------------------------- 1 | obsolete Short proximal phalanx of the ring finger 2 | HP_0009300 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0004355: -------------------------------------------------------------------------------- 1 | obsolete Abnormality of proteoglycan metabolism 2 | HP_0001939 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0004367: -------------------------------------------------------------------------------- 1 | obsolete Abnormality of glycoprotein metabolism 2 | HP_0001939 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0004759: -------------------------------------------------------------------------------- 1 | obsolete Nodular calcific aortic valve disease 2 | 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0004760: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/WGLab/PhenoSV/HEAD/phenosv/Phen2Gene/outdated_HP/HP_0004760 -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0004928: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/WGLab/PhenoSV/HEAD/phenosv/Phen2Gene/outdated_HP/HP_0004928 -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0004929: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/WGLab/PhenoSV/HEAD/phenosv/Phen2Gene/outdated_HP/HP_0004929 -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0004953: -------------------------------------------------------------------------------- 1 | obsolete Dilatation of abdominal aorta 2 | HP_0005112 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0004954: -------------------------------------------------------------------------------- 1 | obsolete Dilatation of the descending aorta 2 | HP_0004959 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0004986: -------------------------------------------------------------------------------- 1 | obsolete Rudimentary to absent fibulae 2 | HP_0006381 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0005111: -------------------------------------------------------------------------------- 1 | obsolete Dilatation of the ascending aorta 2 | HP_0004970 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0005114: -------------------------------------------------------------------------------- 1 | obsolete Abnormalities of the peripheral arteries 2 | HP_0011004 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0005130: -------------------------------------------------------------------------------- 1 | obsolete Restrictive heart failure 2 | HP_0001723 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0005141: -------------------------------------------------------------------------------- 1 | obsolete Episodes of ventricular tachycardia 2 | HP_0004751 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0005173: -------------------------------------------------------------------------------- 1 | obsolete Calcific aortic valve stenosis 2 | HP_0004380 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0005296: -------------------------------------------------------------------------------- 1 | obsolete Occlusive vascular disease 2 | HP_0004950 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0005298: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/WGLab/PhenoSV/HEAD/phenosv/Phen2Gene/outdated_HP/HP_0005298 -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0005299: -------------------------------------------------------------------------------- 1 | obsolete Premature peripheral vascular disease 2 | HP_0004950 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0005309: -------------------------------------------------------------------------------- 1 | obsolete Peripheral vascular insufficiency 2 | HP_0004950 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0005315: -------------------------------------------------------------------------------- 1 | obsolete Peripheral artery occlusive disease 2 | HP_0004950 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0005364: -------------------------------------------------------------------------------- 1 | obsolete Severe viral infections 2 | HP_0004429 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0005375: -------------------------------------------------------------------------------- 1 | obsolete Partial cellular immunodeficiency 2 | HP_0005374 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0005379: -------------------------------------------------------------------------------- 1 | obsolete Severe T lymphocytopenia 2 | 3 | HP_0005403 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0005397: -------------------------------------------------------------------------------- 1 | obsolete Exaggerated cellular immune processes 2 | 3 | HP_0011840 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0005402: -------------------------------------------------------------------------------- 1 | obsolete Primary T-lymphocyte immune abnormalities 2 | HP_0011840 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0005409: -------------------------------------------------------------------------------- 1 | obsolete Markedly reduced T cell function 2 | HP_0005435 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0005549: -------------------------------------------------------------------------------- 1 | obsolete Congenital neutropenia 2 | 3 | HP_0001875 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0005744: -------------------------------------------------------------------------------- 1 | obsolete Generalized osteoporosis with pathologic fractures 2 | HP_0040160 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0005794: -------------------------------------------------------------------------------- 1 | obsolete Arterial disease of legs 2 | HP_0004950 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0005833: -------------------------------------------------------------------------------- 1 | obsolete Joint swelling onset late infancy 2 | 3 | HP_0001386 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0005834: -------------------------------------------------------------------------------- 1 | obsolete Thumbs hypo/aplastic 2 | HP_0009658 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0005837: -------------------------------------------------------------------------------- 1 | obsolete Joint dislocations in young adult 2 | HP_0001373 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0005901: -------------------------------------------------------------------------------- 1 | obsolete Chronic recurrent multifocal osteomyelitis 2 | HP_0002754 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0005921: -------------------------------------------------------------------------------- 1 | obsolete Abnormal ossification of hand bones 2 | HP_0010660 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0006158: -------------------------------------------------------------------------------- 1 | obsolete Finger joint hyperextensibility 2 | 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0006525: -------------------------------------------------------------------------------- 1 | obsolete Lung segmentation defects 2 | HP_0002101 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0006830: -------------------------------------------------------------------------------- 1 | obsolete Severe neonatal hypotonia in males 2 | 3 | HP_0001319 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0006877: -------------------------------------------------------------------------------- 1 | obsolete Mental retardation, in some 2 | HP_0001249 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0007087: -------------------------------------------------------------------------------- 1 | obsolete Involuntary jerking movements 2 | HP_0001336 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0007163: -------------------------------------------------------------------------------- 1 | obsolete Corticospinal tract disease in lower limbs 2 | 3 | HP_0007256 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0007314: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/WGLab/PhenoSV/HEAD/phenosv/Phen2Gene/outdated_HP/HP_0007314 -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0007316: -------------------------------------------------------------------------------- 1 | obsolete Involuntary writhing movements 2 | HP_0002305 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0007409: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/WGLab/PhenoSV/HEAD/phenosv/Phen2Gene/outdated_HP/HP_0007409 -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0007654: -------------------------------------------------------------------------------- 1 | obsolete Retinal striation 2 | 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0007659: -------------------------------------------------------------------------------- 1 | obsolete Decreased retinal pigmentation with dispersion 2 | 3 | HP_0007703 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0007691: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/WGLab/PhenoSV/HEAD/phenosv/Phen2Gene/outdated_HP/HP_0007691 -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0007692: -------------------------------------------------------------------------------- 1 | obsolete Nonnuclear polymorphic congenital cataract 2 | HP_0000519 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0007698: -------------------------------------------------------------------------------- 1 | obsolete Retinal pigment epithelial atrophy 2 | 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0007702: -------------------------------------------------------------------------------- 1 | obsolete Pigmentary retinal deposits 2 | HP_0000580 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0007712: -------------------------------------------------------------------------------- 1 | obsolete Choroidal dystrophy 2 | 3 | HP_0001135 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0007713: -------------------------------------------------------------------------------- 1 | obsolete Juvenile zonular cataracts 2 | HP_0010920 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0007736: -------------------------------------------------------------------------------- 1 | obsolete Pericentral retinal dystrophy 2 | 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0007739: -------------------------------------------------------------------------------- 1 | obsolete Mildly reduced visual acuity 2 | HP_0007663 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0007744: -------------------------------------------------------------------------------- 1 | obsolete Iridoretinal coloboma 2 | 3 | HP_0000612 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0007748: -------------------------------------------------------------------------------- 1 | obsolete Irido-fundal coloboma 2 | 3 | HP_0000612 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0007756: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/WGLab/PhenoSV/HEAD/phenosv/Phen2Gene/outdated_HP/HP_0007756 -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0007757: -------------------------------------------------------------------------------- 1 | obsolete Hypoplasia of choroid 2 | HP_0000610 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0007758: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/WGLab/PhenoSV/HEAD/phenosv/Phen2Gene/outdated_HP/HP_0007758 -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0007782: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/WGLab/PhenoSV/HEAD/phenosv/Phen2Gene/outdated_HP/HP_0007782 -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0007783: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/WGLab/PhenoSV/HEAD/phenosv/Phen2Gene/outdated_HP/HP_0007783 -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0007786: -------------------------------------------------------------------------------- 1 | obsolete Lacunar retinal depigmentation 2 | 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0007798: -------------------------------------------------------------------------------- 1 | obsolete Foveal dystrophy 2 | 3 | HP_0000493 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0007801: -------------------------------------------------------------------------------- 1 | obsolete Fishnet retinal pigmentation 2 | 3 | HP_0007703 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0007808: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/WGLab/PhenoSV/HEAD/phenosv/Phen2Gene/outdated_HP/HP_0007808 -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0007810: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/WGLab/PhenoSV/HEAD/phenosv/Phen2Gene/outdated_HP/HP_0007810 -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0007825: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/WGLab/PhenoSV/HEAD/phenosv/Phen2Gene/outdated_HP/HP_0007825 -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0007829: -------------------------------------------------------------------------------- 1 | obsolete Diffuse retinal cone degeneration 2 | 3 | HP_0000546 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0007851: -------------------------------------------------------------------------------- 1 | obsolete Temporal displacement of maculae 2 | 3 | HP_0001103 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0007852: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/WGLab/PhenoSV/HEAD/phenosv/Phen2Gene/outdated_HP/HP_0007852 -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0007868: -------------------------------------------------------------------------------- 1 | obsolete Age-related macular degeneration 2 | 3 | HP_0000608 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0007869: -------------------------------------------------------------------------------- 1 | obsolete Peripheral retinopathy 2 | 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0007876: -------------------------------------------------------------------------------- 1 | obsolete Juvenile cortical cataract 2 | HP_0100019 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0007893: -------------------------------------------------------------------------------- 1 | obsolete Progressive retinal degeneration 2 | 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0007901: -------------------------------------------------------------------------------- 1 | obsolete Retinal malformation 2 | HP_0000479 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0007910: -------------------------------------------------------------------------------- 1 | obsolete Nonprogressive congenital retinal dystrophy 2 | 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0007916: -------------------------------------------------------------------------------- 1 | obsolete Small anterior lens surface opacities 2 | 3 | HP_0007795 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0007920: -------------------------------------------------------------------------------- 1 | obsolete Congenital chorioretinal dystrophy 2 | HP_0001135 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0007923: -------------------------------------------------------------------------------- 1 | obsolete Foveal hyperplasia 2 | 3 | HP_0000493 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0007930: -------------------------------------------------------------------------------- 1 | obsolete Prominent epicanthal folds 2 | HP_0000286 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0007945: -------------------------------------------------------------------------------- 1 | obsolete Choroidal degeneration 2 | 3 | HP_0200065 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0007949: -------------------------------------------------------------------------------- 1 | obsolete Progressive macular scarring 2 | 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0007956: -------------------------------------------------------------------------------- 1 | obsolete Bilateral choroid coloboma 2 | HP_0000567 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0007961: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/WGLab/PhenoSV/HEAD/phenosv/Phen2Gene/outdated_HP/HP_0007961 -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0007981: -------------------------------------------------------------------------------- 1 | obsolete Concentric narrowing of visual field 2 | HP_0001133 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0007982: -------------------------------------------------------------------------------- 1 | obsolete Central tapetoretinal dystrophy 2 | 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0008008: -------------------------------------------------------------------------------- 1 | obsolete Progressive central visual loss 2 | 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0008012: -------------------------------------------------------------------------------- 1 | obsolete Congenital myopia 2 | 3 | HP_0000545 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0008017: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/WGLab/PhenoSV/HEAD/phenosv/Phen2Gene/outdated_HP/HP_0008017 -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0008024: -------------------------------------------------------------------------------- 1 | obsolete Congenital nuclear cataract 2 | HP_0100018 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0008033: -------------------------------------------------------------------------------- 1 | obsolete Congenital exotropia 2 | HP_0000577 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0008036: -------------------------------------------------------------------------------- 1 | obsolete Rod-cone dystrophy 2 | 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0008051: -------------------------------------------------------------------------------- 1 | obsolete Abnormality of the retinal pigment epithelium 2 | HP_0007703 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0008230: -------------------------------------------------------------------------------- 1 | obsolete Decreased testosterone in males 2 | HP_0040171 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0008356: -------------------------------------------------------------------------------- 1 | obsolete Combined hyperlipidemia 2 | 3 | HP_0003077 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0008694: -------------------------------------------------------------------------------- 1 | obsolete Hypertrophic labia minora 2 | 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0009044: -------------------------------------------------------------------------------- 1 | obsolete Hypoplasia of deltoid muscle 2 | HP_0030241 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0009090: -------------------------------------------------------------------------------- 1 | obsolete Facial diplegic appearance 2 | 3 | HP_0001349 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0009163: -------------------------------------------------------------------------------- 1 | obsolete Abnormal form of the 5th finger 2 | 3 | HP_0004207 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0009448: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/WGLab/PhenoSV/HEAD/phenosv/Phen2Gene/outdated_HP/HP_0009448 -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0009449: -------------------------------------------------------------------------------- 1 | obsolete Hypoplastic/small phalanges of the 3rd finger 2 | HP_0009447 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0009620: -------------------------------------------------------------------------------- 1 | obsolete Radial deviation of the thumb 2 | 3 | HP_0009602 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0009621: -------------------------------------------------------------------------------- 1 | obsolete Ulnar deviation of the thumb 2 | 3 | HP_0009602 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0009885: -------------------------------------------------------------------------------- 1 | obsolete Prenatal short stature 2 | 3 | HP_0001511 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0010700: -------------------------------------------------------------------------------- 1 | obsolete Total cataract 2 | HP_0000518 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0010905: -------------------------------------------------------------------------------- 1 | obsolete Abnormality of histidine metabolism 2 | HP_0010904 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0010928: -------------------------------------------------------------------------------- 1 | obsolete Increased urinary orotic acid concentration 2 | HP_0003218 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0011146: -------------------------------------------------------------------------------- 1 | obsolete Dialeptic seizures 2 | HP_0002384 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0011148: -------------------------------------------------------------------------------- 1 | obsolete Absence seizures with special features 2 | HP_0002121 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0011498: -------------------------------------------------------------------------------- 1 | obsolete Partial aniridia 2 | HP_0000526 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0011606: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/WGLab/PhenoSV/HEAD/phenosv/Phen2Gene/outdated_HP/HP_0011606 -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0011607: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/WGLab/PhenoSV/HEAD/phenosv/Phen2Gene/outdated_HP/HP_0011607 -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0011765: -------------------------------------------------------------------------------- 1 | obsolete Ectopic anterior pituitary 2 | HP_0012731 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0012140: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/WGLab/PhenoSV/HEAD/phenosv/Phen2Gene/outdated_HP/HP_0012140 -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0012201: -------------------------------------------------------------------------------- 1 | obsolete Reduced prothrombin activity 2 | HP_0008151 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0012291: -------------------------------------------------------------------------------- 1 | obsolete Tracheal neoplasm 2 | HP_0100551 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0012374: -------------------------------------------------------------------------------- 1 | obsolete Abnormal globe morphology 2 | HP_0012372 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0012455: -------------------------------------------------------------------------------- 1 | obsolete Large artery calcification 2 | HP_0003207 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0025462: -------------------------------------------------------------------------------- 1 | obsolete Abnormal cellular physiology 2 | HP_0011017 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0025541: -------------------------------------------------------------------------------- 1 | obsolete Decreased activity of complement receptor 2 | 3 | HP_0005339 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0030013: -------------------------------------------------------------------------------- 1 | obsolete Endometriosis 2 | HP_0030127 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0030073: -------------------------------------------------------------------------------- 1 | obsolete Pharyngeal neoplasm 2 | HP_0100638 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0030152: -------------------------------------------------------------------------------- 1 | obsolete Biliary tract neoplasm 2 | HP_0100574 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0030332: -------------------------------------------------------------------------------- 1 | obsolete Abnormal T cell morphology 2 | HP_0002843 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0030340: -------------------------------------------------------------------------------- 1 | obsolete Increased circulating gonadotropin level 2 | HP_0000837 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0030422: -------------------------------------------------------------------------------- 1 | obsolete Papillary cystadenoma of the epididymis 2 | 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0030523: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/WGLab/PhenoSV/HEAD/phenosv/Phen2Gene/outdated_HP/HP_0030523 -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0030524: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/WGLab/PhenoSV/HEAD/phenosv/Phen2Gene/outdated_HP/HP_0030524 -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0030761: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/WGLab/PhenoSV/HEAD/phenosv/Phen2Gene/outdated_HP/HP_0030761 -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0030960: -------------------------------------------------------------------------------- 1 | obsolete Abnormal pupillary morphology 2 | HP_0000615 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0030963: -------------------------------------------------------------------------------- 1 | obsolete Abnormal aortic morphology 2 | HP_0001679 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0030971: -------------------------------------------------------------------------------- 1 | obsolete Abnormal vena cava morphology 2 | HP_0005345 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0031440: -------------------------------------------------------------------------------- 1 | obsolete Abnormal tricuspid valve morphology 2 | HP_0001702 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0031477: -------------------------------------------------------------------------------- 1 | obsolete Abnormal mitral valve morphology 2 | HP_0001633 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0031988: -------------------------------------------------------------------------------- 1 | obsolete Muscle spasm 2 | HP_0003394 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0040037: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/WGLab/PhenoSV/HEAD/phenosv/Phen2Gene/outdated_HP/HP_0040037 -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0040038: -------------------------------------------------------------------------------- 1 | obsolete Thin toenail 2 | HP_0012746 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0040077: -------------------------------------------------------------------------------- 1 | obsolete Abnormal concentration of calcium in blood 2 | HP_0004363 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0040193: -------------------------------------------------------------------------------- 1 | obsolete Pinealoblastoma 2 | HP_0030408 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0040199: -------------------------------------------------------------------------------- 1 | obsolete Flat midface 2 | HP_0011800 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0040316: -------------------------------------------------------------------------------- 1 | obsolete Aplasia of the penis 2 | HP_0030261 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0045013: -------------------------------------------------------------------------------- 1 | obsolete Decreased urinary glucose concentration 2 | 3 | HP_0011016 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0045016: -------------------------------------------------------------------------------- 1 | obsolete Elevated serum long-chain fatty acids 2 | HP_0003455 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0045083: -------------------------------------------------------------------------------- 1 | obsolete Increased body mass index 2 | 3 | HP_0004324 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0100609: -------------------------------------------------------------------------------- 1 | obsolete Hypermenorrhea 2 | HP_0000132 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0100637: -------------------------------------------------------------------------------- 1 | obsolete Neoplasia of the nose 2 | HP_0012720 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0100805: -------------------------------------------------------------------------------- 1 | obsolete Precocious menopause 2 | 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0100843: -------------------------------------------------------------------------------- 1 | obsolete Glioblastoma 2 | HP_0012174 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0200099: -------------------------------------------------------------------------------- 1 | obsolete Peripheral retinal pigmentation abnormalities 2 | 3 | HP_0007703 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0200126: -------------------------------------------------------------------------------- 1 | obsolete Amyloid cardiomyopathy 2 | HP_0030843 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0200129: -------------------------------------------------------------------------------- 1 | obsolete Calcific mitral stenosis 2 | 3 | HP_0001718 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0200135: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/WGLab/PhenoSV/HEAD/phenosv/Phen2Gene/outdated_HP/HP_0200135 -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0200144: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/WGLab/PhenoSV/HEAD/phenosv/Phen2Gene/outdated_HP/HP_0200144 -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0410004: -------------------------------------------------------------------------------- 1 | obsolete Cleft secondary palate 2 | HP_0000175 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0500010: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/WGLab/PhenoSV/HEAD/phenosv/Phen2Gene/outdated_HP/HP_0500010 -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_0500014: -------------------------------------------------------------------------------- 1 | obsolete Abnormal test result 2 | 3 | HP_0000118 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_3000001: -------------------------------------------------------------------------------- 1 | obsolete Abnormal heart morphology 2 | HP_0001627 3 | 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/outdated_HP/HP_3000026: -------------------------------------------------------------------------------- 1 | obsolete Abnormality of common carotid artery plus branches 2 | 3 | HP_0430021 4 | -------------------------------------------------------------------------------- /phenosv/Phen2Gene/output.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/WGLab/PhenoSV/HEAD/phenosv/Phen2Gene/output.py -------------------------------------------------------------------------------- /phenosv/Phen2Gene/phen2gene.py: 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