├── .gitignore ├── C_tools ├── README.md ├── apue.h ├── fq_gc_filter ├── fq_gc_filter.c ├── fq_stat ├── fq_stat.c ├── kseq.h ├── out └── split_bam_by_barcode.c ├── HiC ├── ALLHiC │ ├── README.md │ ├── Snakefile │ └── config.yaml ├── YaHS │ ├── Snakefile │ └── config.yaml ├── hic_pro_pre.sh ├── hicpro2juicebox.sh ├── hicpro2salsa.sh ├── run_3d_pipeline.sh └── run_hicexplorer_pipeline.sh ├── README.md ├── STAR_counts.sh ├── annotation ├── STAR_StringTie.sh ├── aa2nonred.pl ├── add_annotation_from_dat.py ├── annnotation_version_conversion.ipynb ├── annotate_cds_in_transcripts.sh ├── cds2gtf.py ├── compute_flanking_region.pl ├── find_homology.py ├── gene_rename.py ├── get_the_longest_transcripts.py ├── get_the_trainning_sets.py ├── gff2bed.R ├── gff2bed12.py ├── gff2gtf.py ├── gff3_preds2models ├── gff3_select ├── gff_update.py ├── ltr_retreiver.sh ├── maker2apollo.sh ├── maker_filter.py ├── maker_rename.py ├── maker_stats.R ├── quick_anno_with_gmap.sh └── unified_peak.py ├── assembly ├── find_contaimation.sh ├── nextpolish.sh ├── pb_polish.sh └── purge_dup.sh ├── assembly2agp.py ├── bed12togtf.pl ├── bsa_upstream.sh ├── calc_depth_from_cov.py ├── calculate_4DTV_correction.pl ├── colors.txt ├── comparative ├── MSA │ ├── combine_msa.py │ ├── extract_seq_by_OG.py │ └── snakefile ├── clade_and_size_filter.py ├── draw_cafe_tree.py ├── generate_conf.py ├── mcmctree_helper.py ├── prep_r8s.py ├── wgdi_helper.py ├── wgdi_homo.py ├── wgdi_links.py ├── wgdi_reverse.py └── wgdi_simple.py ├── eblastn.sh ├── get_asm_stats.py ├── igv_web.py ├── kseq.h ├── misc ├── bam_utils.py ├── fastx_stat.py ├── gff_utils.py ├── myBlat.py ├── snp_calling.sh └── splite_super_big_genome.py ├── mummplot.R ├── pdf2jpg.py ├── pipeline ├── ATAC │ ├── .vscode │ │ ├── c_cpp_properties.json │ │ ├── launch.json │ │ ├── settings.json │ │ └── tasks.json │ ├── README.md │ ├── Snakefile │ ├── bam_basic_stats.c │ ├── bam_frag_stats.c │ ├── config.yaml │ ├── env.yaml │ └── samples.csv ├── BS-Seq │ ├── Snakefile │ ├── config.yaml │ ├── envs │ │ ├── bismark.yaml │ │ └── qc.yaml │ └── samples.txt ├── mbs │ ├── Snakefile │ ├── config.yaml │ └── script │ │ ├── Athaliana_chr_len.tsv │ │ ├── find_insertion.sh │ │ ├── gene_description_20131231.tsv │ │ └── snp_filter.R ├── population-snp-calling-BCFtools │ ├── README.md │ ├── Snakefile │ ├── config.yaml │ └── env.yaml ├── population-snp-calling-GATK │ ├── README.md │ ├── Snakefile │ ├── config.yaml │ └── env.yaml ├── rna-seq-upstream │ ├── Snakefile │ └── config.yaml └── transcriptome-assembly-pipeline │ ├── Snakefile │ ├── __pycache__ │ └── trinity_post_process_v2.cpython-310.pyc │ ├── best_gene.fasta │ ├── coverage.tsv │ ├── coverage_plot.png │ ├── explore copy.ipynb │ ├── explore.ipynb │ ├── trinity_post_process.py │ └── trinity_post_process_v2.py ├── simple2links.py ├── split_fa_by_id.c ├── t_dna_analysis.py ├── vcf_slimming.py ├── visTree.R ├── wechat_article_parser.py └── zgtools.R /.gitignore: -------------------------------------------------------------------------------- 1 | .vscode 2 | -------------------------------------------------------------------------------- /C_tools/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/C_tools/README.md -------------------------------------------------------------------------------- /C_tools/apue.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/C_tools/apue.h -------------------------------------------------------------------------------- /C_tools/fq_gc_filter: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/C_tools/fq_gc_filter -------------------------------------------------------------------------------- /C_tools/fq_gc_filter.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/C_tools/fq_gc_filter.c -------------------------------------------------------------------------------- /C_tools/fq_stat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/C_tools/fq_stat -------------------------------------------------------------------------------- /C_tools/fq_stat.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/C_tools/fq_stat.c -------------------------------------------------------------------------------- /C_tools/kseq.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/C_tools/kseq.h -------------------------------------------------------------------------------- /C_tools/out: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/C_tools/out -------------------------------------------------------------------------------- /C_tools/split_bam_by_barcode.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/C_tools/split_bam_by_barcode.c -------------------------------------------------------------------------------- /HiC/ALLHiC/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/HiC/ALLHiC/README.md -------------------------------------------------------------------------------- /HiC/ALLHiC/Snakefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/HiC/ALLHiC/Snakefile -------------------------------------------------------------------------------- /HiC/ALLHiC/config.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/HiC/ALLHiC/config.yaml -------------------------------------------------------------------------------- /HiC/YaHS/Snakefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/HiC/YaHS/Snakefile -------------------------------------------------------------------------------- /HiC/YaHS/config.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/HiC/YaHS/config.yaml -------------------------------------------------------------------------------- /HiC/hic_pro_pre.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/HiC/hic_pro_pre.sh -------------------------------------------------------------------------------- /HiC/hicpro2juicebox.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/HiC/hicpro2juicebox.sh -------------------------------------------------------------------------------- /HiC/hicpro2salsa.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/HiC/hicpro2salsa.sh -------------------------------------------------------------------------------- /HiC/run_3d_pipeline.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/HiC/run_3d_pipeline.sh -------------------------------------------------------------------------------- /HiC/run_hicexplorer_pipeline.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/HiC/run_hicexplorer_pipeline.sh -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/README.md -------------------------------------------------------------------------------- /STAR_counts.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/STAR_counts.sh -------------------------------------------------------------------------------- /annotation/STAR_StringTie.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/annotation/STAR_StringTie.sh -------------------------------------------------------------------------------- /annotation/aa2nonred.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/annotation/aa2nonred.pl -------------------------------------------------------------------------------- /annotation/add_annotation_from_dat.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/annotation/add_annotation_from_dat.py -------------------------------------------------------------------------------- /annotation/annnotation_version_conversion.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/annotation/annnotation_version_conversion.ipynb -------------------------------------------------------------------------------- /annotation/annotate_cds_in_transcripts.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/annotation/annotate_cds_in_transcripts.sh -------------------------------------------------------------------------------- /annotation/cds2gtf.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/annotation/cds2gtf.py -------------------------------------------------------------------------------- /annotation/compute_flanking_region.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/annotation/compute_flanking_region.pl -------------------------------------------------------------------------------- /annotation/find_homology.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/annotation/find_homology.py -------------------------------------------------------------------------------- /annotation/gene_rename.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/annotation/gene_rename.py -------------------------------------------------------------------------------- /annotation/get_the_longest_transcripts.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/annotation/get_the_longest_transcripts.py -------------------------------------------------------------------------------- /annotation/get_the_trainning_sets.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/annotation/get_the_trainning_sets.py -------------------------------------------------------------------------------- /annotation/gff2bed.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/annotation/gff2bed.R -------------------------------------------------------------------------------- /annotation/gff2bed12.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/annotation/gff2bed12.py -------------------------------------------------------------------------------- /annotation/gff2gtf.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/annotation/gff2gtf.py -------------------------------------------------------------------------------- /annotation/gff3_preds2models: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/annotation/gff3_preds2models -------------------------------------------------------------------------------- /annotation/gff3_select: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/annotation/gff3_select -------------------------------------------------------------------------------- /annotation/gff_update.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/annotation/gff_update.py -------------------------------------------------------------------------------- /annotation/ltr_retreiver.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/annotation/ltr_retreiver.sh -------------------------------------------------------------------------------- /annotation/maker2apollo.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/annotation/maker2apollo.sh -------------------------------------------------------------------------------- /annotation/maker_filter.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/annotation/maker_filter.py -------------------------------------------------------------------------------- /annotation/maker_rename.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/annotation/maker_rename.py -------------------------------------------------------------------------------- /annotation/maker_stats.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/annotation/maker_stats.R -------------------------------------------------------------------------------- /annotation/quick_anno_with_gmap.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/annotation/quick_anno_with_gmap.sh -------------------------------------------------------------------------------- /annotation/unified_peak.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/annotation/unified_peak.py -------------------------------------------------------------------------------- /assembly/find_contaimation.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/assembly/find_contaimation.sh -------------------------------------------------------------------------------- /assembly/nextpolish.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/assembly/nextpolish.sh -------------------------------------------------------------------------------- /assembly/pb_polish.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/assembly/pb_polish.sh -------------------------------------------------------------------------------- /assembly/purge_dup.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/assembly/purge_dup.sh -------------------------------------------------------------------------------- /assembly2agp.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/assembly2agp.py -------------------------------------------------------------------------------- /bed12togtf.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/bed12togtf.pl -------------------------------------------------------------------------------- /bsa_upstream.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/bsa_upstream.sh -------------------------------------------------------------------------------- /calc_depth_from_cov.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/calc_depth_from_cov.py -------------------------------------------------------------------------------- /calculate_4DTV_correction.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/calculate_4DTV_correction.pl -------------------------------------------------------------------------------- /colors.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/colors.txt -------------------------------------------------------------------------------- /comparative/MSA/combine_msa.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/comparative/MSA/combine_msa.py -------------------------------------------------------------------------------- /comparative/MSA/extract_seq_by_OG.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/comparative/MSA/extract_seq_by_OG.py -------------------------------------------------------------------------------- /comparative/MSA/snakefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/comparative/MSA/snakefile -------------------------------------------------------------------------------- /comparative/clade_and_size_filter.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/comparative/clade_and_size_filter.py -------------------------------------------------------------------------------- /comparative/draw_cafe_tree.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/comparative/draw_cafe_tree.py -------------------------------------------------------------------------------- /comparative/generate_conf.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/comparative/generate_conf.py -------------------------------------------------------------------------------- /comparative/mcmctree_helper.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/comparative/mcmctree_helper.py -------------------------------------------------------------------------------- /comparative/prep_r8s.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/comparative/prep_r8s.py -------------------------------------------------------------------------------- /comparative/wgdi_helper.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/comparative/wgdi_helper.py -------------------------------------------------------------------------------- /comparative/wgdi_homo.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/comparative/wgdi_homo.py -------------------------------------------------------------------------------- /comparative/wgdi_links.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/comparative/wgdi_links.py -------------------------------------------------------------------------------- /comparative/wgdi_reverse.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/comparative/wgdi_reverse.py -------------------------------------------------------------------------------- /comparative/wgdi_simple.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/comparative/wgdi_simple.py -------------------------------------------------------------------------------- /eblastn.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/eblastn.sh -------------------------------------------------------------------------------- /get_asm_stats.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/get_asm_stats.py -------------------------------------------------------------------------------- /igv_web.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/igv_web.py -------------------------------------------------------------------------------- /kseq.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/kseq.h -------------------------------------------------------------------------------- /misc/bam_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/misc/bam_utils.py -------------------------------------------------------------------------------- /misc/fastx_stat.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/misc/fastx_stat.py -------------------------------------------------------------------------------- /misc/gff_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/misc/gff_utils.py -------------------------------------------------------------------------------- /misc/myBlat.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/misc/myBlat.py -------------------------------------------------------------------------------- /misc/snp_calling.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/misc/snp_calling.sh -------------------------------------------------------------------------------- /misc/splite_super_big_genome.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/misc/splite_super_big_genome.py -------------------------------------------------------------------------------- /mummplot.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/mummplot.R -------------------------------------------------------------------------------- /pdf2jpg.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/pdf2jpg.py -------------------------------------------------------------------------------- /pipeline/ATAC/.vscode/c_cpp_properties.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/pipeline/ATAC/.vscode/c_cpp_properties.json -------------------------------------------------------------------------------- /pipeline/ATAC/.vscode/launch.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/pipeline/ATAC/.vscode/launch.json -------------------------------------------------------------------------------- /pipeline/ATAC/.vscode/settings.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/pipeline/ATAC/.vscode/settings.json -------------------------------------------------------------------------------- /pipeline/ATAC/.vscode/tasks.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/pipeline/ATAC/.vscode/tasks.json -------------------------------------------------------------------------------- /pipeline/ATAC/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/pipeline/ATAC/README.md -------------------------------------------------------------------------------- /pipeline/ATAC/Snakefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/pipeline/ATAC/Snakefile -------------------------------------------------------------------------------- /pipeline/ATAC/bam_basic_stats.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/pipeline/ATAC/bam_basic_stats.c -------------------------------------------------------------------------------- /pipeline/ATAC/bam_frag_stats.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/pipeline/ATAC/bam_frag_stats.c -------------------------------------------------------------------------------- /pipeline/ATAC/config.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/pipeline/ATAC/config.yaml -------------------------------------------------------------------------------- /pipeline/ATAC/env.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/pipeline/ATAC/env.yaml -------------------------------------------------------------------------------- /pipeline/ATAC/samples.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/pipeline/ATAC/samples.csv -------------------------------------------------------------------------------- /pipeline/BS-Seq/Snakefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/pipeline/BS-Seq/Snakefile -------------------------------------------------------------------------------- /pipeline/BS-Seq/config.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/pipeline/BS-Seq/config.yaml -------------------------------------------------------------------------------- /pipeline/BS-Seq/envs/bismark.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/pipeline/BS-Seq/envs/bismark.yaml -------------------------------------------------------------------------------- /pipeline/BS-Seq/envs/qc.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/pipeline/BS-Seq/envs/qc.yaml -------------------------------------------------------------------------------- /pipeline/BS-Seq/samples.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/pipeline/BS-Seq/samples.txt -------------------------------------------------------------------------------- /pipeline/mbs/Snakefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/pipeline/mbs/Snakefile -------------------------------------------------------------------------------- /pipeline/mbs/config.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/pipeline/mbs/config.yaml -------------------------------------------------------------------------------- /pipeline/mbs/script/Athaliana_chr_len.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/pipeline/mbs/script/Athaliana_chr_len.tsv -------------------------------------------------------------------------------- /pipeline/mbs/script/find_insertion.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/pipeline/mbs/script/find_insertion.sh -------------------------------------------------------------------------------- /pipeline/mbs/script/gene_description_20131231.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/pipeline/mbs/script/gene_description_20131231.tsv -------------------------------------------------------------------------------- /pipeline/mbs/script/snp_filter.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/pipeline/mbs/script/snp_filter.R -------------------------------------------------------------------------------- /pipeline/population-snp-calling-BCFtools/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/pipeline/population-snp-calling-BCFtools/README.md -------------------------------------------------------------------------------- /pipeline/population-snp-calling-BCFtools/Snakefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/pipeline/population-snp-calling-BCFtools/Snakefile -------------------------------------------------------------------------------- /pipeline/population-snp-calling-BCFtools/config.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/pipeline/population-snp-calling-BCFtools/config.yaml -------------------------------------------------------------------------------- /pipeline/population-snp-calling-BCFtools/env.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/pipeline/population-snp-calling-BCFtools/env.yaml -------------------------------------------------------------------------------- /pipeline/population-snp-calling-GATK/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/pipeline/population-snp-calling-GATK/README.md -------------------------------------------------------------------------------- /pipeline/population-snp-calling-GATK/Snakefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/pipeline/population-snp-calling-GATK/Snakefile -------------------------------------------------------------------------------- /pipeline/population-snp-calling-GATK/config.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/pipeline/population-snp-calling-GATK/config.yaml -------------------------------------------------------------------------------- /pipeline/population-snp-calling-GATK/env.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/pipeline/population-snp-calling-GATK/env.yaml -------------------------------------------------------------------------------- /pipeline/rna-seq-upstream/Snakefile: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /pipeline/rna-seq-upstream/config.yaml: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /pipeline/transcriptome-assembly-pipeline/Snakefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/pipeline/transcriptome-assembly-pipeline/Snakefile -------------------------------------------------------------------------------- /pipeline/transcriptome-assembly-pipeline/__pycache__/trinity_post_process_v2.cpython-310.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/pipeline/transcriptome-assembly-pipeline/__pycache__/trinity_post_process_v2.cpython-310.pyc -------------------------------------------------------------------------------- /pipeline/transcriptome-assembly-pipeline/best_gene.fasta: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/pipeline/transcriptome-assembly-pipeline/best_gene.fasta -------------------------------------------------------------------------------- /pipeline/transcriptome-assembly-pipeline/coverage.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/pipeline/transcriptome-assembly-pipeline/coverage.tsv -------------------------------------------------------------------------------- /pipeline/transcriptome-assembly-pipeline/coverage_plot.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/pipeline/transcriptome-assembly-pipeline/coverage_plot.png -------------------------------------------------------------------------------- /pipeline/transcriptome-assembly-pipeline/explore copy.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/pipeline/transcriptome-assembly-pipeline/explore copy.ipynb -------------------------------------------------------------------------------- /pipeline/transcriptome-assembly-pipeline/explore.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/pipeline/transcriptome-assembly-pipeline/explore.ipynb -------------------------------------------------------------------------------- /pipeline/transcriptome-assembly-pipeline/trinity_post_process.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/pipeline/transcriptome-assembly-pipeline/trinity_post_process.py -------------------------------------------------------------------------------- /pipeline/transcriptome-assembly-pipeline/trinity_post_process_v2.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/pipeline/transcriptome-assembly-pipeline/trinity_post_process_v2.py -------------------------------------------------------------------------------- /simple2links.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/simple2links.py -------------------------------------------------------------------------------- /split_fa_by_id.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/split_fa_by_id.c -------------------------------------------------------------------------------- /t_dna_analysis.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/t_dna_analysis.py -------------------------------------------------------------------------------- /vcf_slimming.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/vcf_slimming.py -------------------------------------------------------------------------------- /visTree.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/visTree.R -------------------------------------------------------------------------------- /wechat_article_parser.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/wechat_article_parser.py -------------------------------------------------------------------------------- /zgtools.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xuzhougeng/myscripts/HEAD/zgtools.R --------------------------------------------------------------------------------