├── LICENSE ├── README.md ├── data ├── 41467_2020_16164_MOESM5_ESM.csv ├── PMID: 31924475 ├── README.txt ├── all_cell_markers.txt ├── celltype_PMID30289549.txt ├── celltype_bladder.txt ├── celltype_tcell.txt ├── dbcorc │ ├── PMC10216238.tsv │ ├── RD.tsv │ └── README.md └── sc-example.bam ├── readme ├── src ├── README.md ├── annovar_DNAseq_hg38.sh ├── bash-tools ├── biobert.md ├── bulkrna-jihye.sh ├── bwa-ancient-dna ├── cellranger.sh ├── cluster-seurat.sh ├── cnvkit ├── data_from_scpred.sh ├── deseq.r ├── diffexp.r ├── diffexp.sh ├── fastp-examples.sh ├── fastq.sh ├── gatk ├── gatk-examples.sh ├── gpg.sh ├── harmony.r ├── heatmap.r ├── hpc-gpu-pytorch ├── hpc-python ├── integrate-with-harmony.sh ├── merge-cellranger.sh ├── perl ├── pj-scpolya-01.sh ├── predict-celltype-with-scpred.sh ├── rename_files.sh ├── rsem-calculate-expression.sh ├── rsem-dirty.sh ├── rsem-hisat2.sh ├── rsem-install.sh ├── rsem-prepare-reference-star.sh ├── rsem-star-mouse ├── run-cellranger_mkfastq.sh ├── sam.sh ├── sc-deseq2.r ├── scgpt ├── sequence.sh ├── seurat-findmarkers-example.r ├── seurat-merge-cluster-marker.sh ├── seurat-postanalysis.r ├── sftp.sh ├── sierra.sh ├── singler.r ├── singularity.sh ├── slingshot.r ├── slurm-examples.sh ├── train-celltype-with-scpred.sh └── wsl.sh └── test ├── README.md ├── Screen Shot 2020-12-19 at 5.07.40 PM.png ├── Screen Shot 2020-12-19 at 8.34.18 PM.png ├── pbmc_1.harmony.diff.clusters ├── pbmc_1.harmony.diff.csv.csv ├── pbmc_1.harmony.diff.csv.rcmd ├── pbmc_1.harmony.rds.rcmd ├── pbmc_1.harmony_cluster.rds.rcmd ├── pbmc_1.rda ├── pbmc_1.scpred.rds.rcmd ├── pbmc_2.predict.rds.rcmd ├── pbmc_2.rda └── test-harmony.sh /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hmgene/mudcookies/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hmgene/mudcookies/HEAD/README.md -------------------------------------------------------------------------------- /data/41467_2020_16164_MOESM5_ESM.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hmgene/mudcookies/HEAD/data/41467_2020_16164_MOESM5_ESM.csv -------------------------------------------------------------------------------- /data/PMID: 31924475: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hmgene/mudcookies/HEAD/data/PMID: 31924475 -------------------------------------------------------------------------------- /data/README.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hmgene/mudcookies/HEAD/data/README.txt -------------------------------------------------------------------------------- /data/all_cell_markers.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hmgene/mudcookies/HEAD/data/all_cell_markers.txt -------------------------------------------------------------------------------- /data/celltype_PMID30289549.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hmgene/mudcookies/HEAD/data/celltype_PMID30289549.txt -------------------------------------------------------------------------------- /data/celltype_bladder.txt: -------------------------------------------------------------------------------- 1 | #to do 2 | https://www.nature.com/articles/s41586-020-3034-x 3 | i did 4 | -------------------------------------------------------------------------------- /data/celltype_tcell.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hmgene/mudcookies/HEAD/data/celltype_tcell.txt -------------------------------------------------------------------------------- /data/dbcorc/PMC10216238.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hmgene/mudcookies/HEAD/data/dbcorc/PMC10216238.tsv -------------------------------------------------------------------------------- /data/dbcorc/RD.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hmgene/mudcookies/HEAD/data/dbcorc/RD.tsv -------------------------------------------------------------------------------- /data/dbcorc/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hmgene/mudcookies/HEAD/data/dbcorc/README.md -------------------------------------------------------------------------------- /data/sc-example.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hmgene/mudcookies/HEAD/data/sc-example.bam -------------------------------------------------------------------------------- /readme: -------------------------------------------------------------------------------- 1 | dd 2 | -------------------------------------------------------------------------------- /src/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hmgene/mudcookies/HEAD/src/README.md -------------------------------------------------------------------------------- /src/annovar_DNAseq_hg38.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hmgene/mudcookies/HEAD/src/annovar_DNAseq_hg38.sh -------------------------------------------------------------------------------- /src/bash-tools: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hmgene/mudcookies/HEAD/src/bash-tools -------------------------------------------------------------------------------- /src/biobert.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hmgene/mudcookies/HEAD/src/biobert.md -------------------------------------------------------------------------------- /src/bulkrna-jihye.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hmgene/mudcookies/HEAD/src/bulkrna-jihye.sh -------------------------------------------------------------------------------- /src/bwa-ancient-dna: -------------------------------------------------------------------------------- 1 | # read : https://onlinelibrary.wiley.com/doi/full/10.1002/ece3.7056 2 | -------------------------------------------------------------------------------- /src/cellranger.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hmgene/mudcookies/HEAD/src/cellranger.sh -------------------------------------------------------------------------------- /src/cluster-seurat.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hmgene/mudcookies/HEAD/src/cluster-seurat.sh -------------------------------------------------------------------------------- /src/cnvkit: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hmgene/mudcookies/HEAD/src/cnvkit -------------------------------------------------------------------------------- /src/data_from_scpred.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hmgene/mudcookies/HEAD/src/data_from_scpred.sh -------------------------------------------------------------------------------- /src/deseq.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hmgene/mudcookies/HEAD/src/deseq.r -------------------------------------------------------------------------------- /src/diffexp.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hmgene/mudcookies/HEAD/src/diffexp.r -------------------------------------------------------------------------------- /src/diffexp.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hmgene/mudcookies/HEAD/src/diffexp.sh -------------------------------------------------------------------------------- /src/fastp-examples.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hmgene/mudcookies/HEAD/src/fastp-examples.sh -------------------------------------------------------------------------------- /src/fastq.sh: -------------------------------------------------------------------------------- 1 | ## bamToFastq: https://www.biostars.org/p/303752/ 2 | -------------------------------------------------------------------------------- /src/gatk: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hmgene/mudcookies/HEAD/src/gatk -------------------------------------------------------------------------------- /src/gatk-examples.sh: -------------------------------------------------------------------------------- 1 | ## 고맙습니다. GATK 잘 돌아가는 pipeline example 부탁합니다. 2 | ## 기여하신 분들 이름이나 github 등 남겨주세요. 3 | -------------------------------------------------------------------------------- /src/gpg.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hmgene/mudcookies/HEAD/src/gpg.sh -------------------------------------------------------------------------------- /src/harmony.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hmgene/mudcookies/HEAD/src/harmony.r -------------------------------------------------------------------------------- /src/heatmap.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hmgene/mudcookies/HEAD/src/heatmap.r -------------------------------------------------------------------------------- /src/hpc-gpu-pytorch: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hmgene/mudcookies/HEAD/src/hpc-gpu-pytorch -------------------------------------------------------------------------------- /src/hpc-python: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hmgene/mudcookies/HEAD/src/hpc-python -------------------------------------------------------------------------------- /src/integrate-with-harmony.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hmgene/mudcookies/HEAD/src/integrate-with-harmony.sh -------------------------------------------------------------------------------- /src/merge-cellranger.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hmgene/mudcookies/HEAD/src/merge-cellranger.sh -------------------------------------------------------------------------------- /src/perl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hmgene/mudcookies/HEAD/src/perl -------------------------------------------------------------------------------- /src/pj-scpolya-01.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hmgene/mudcookies/HEAD/src/pj-scpolya-01.sh -------------------------------------------------------------------------------- /src/predict-celltype-with-scpred.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hmgene/mudcookies/HEAD/src/predict-celltype-with-scpred.sh -------------------------------------------------------------------------------- /src/rename_files.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hmgene/mudcookies/HEAD/src/rename_files.sh -------------------------------------------------------------------------------- /src/rsem-calculate-expression.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hmgene/mudcookies/HEAD/src/rsem-calculate-expression.sh -------------------------------------------------------------------------------- /src/rsem-dirty.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hmgene/mudcookies/HEAD/src/rsem-dirty.sh -------------------------------------------------------------------------------- /src/rsem-hisat2.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hmgene/mudcookies/HEAD/src/rsem-hisat2.sh -------------------------------------------------------------------------------- /src/rsem-install.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hmgene/mudcookies/HEAD/src/rsem-install.sh -------------------------------------------------------------------------------- /src/rsem-prepare-reference-star.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hmgene/mudcookies/HEAD/src/rsem-prepare-reference-star.sh -------------------------------------------------------------------------------- /src/rsem-star-mouse: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hmgene/mudcookies/HEAD/src/rsem-star-mouse -------------------------------------------------------------------------------- /src/run-cellranger_mkfastq.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hmgene/mudcookies/HEAD/src/run-cellranger_mkfastq.sh -------------------------------------------------------------------------------- /src/sam.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hmgene/mudcookies/HEAD/src/sam.sh -------------------------------------------------------------------------------- /src/sc-deseq2.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hmgene/mudcookies/HEAD/src/sc-deseq2.r -------------------------------------------------------------------------------- /src/scgpt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hmgene/mudcookies/HEAD/src/scgpt -------------------------------------------------------------------------------- /src/sequence.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hmgene/mudcookies/HEAD/src/sequence.sh -------------------------------------------------------------------------------- /src/seurat-findmarkers-example.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hmgene/mudcookies/HEAD/src/seurat-findmarkers-example.r -------------------------------------------------------------------------------- /src/seurat-merge-cluster-marker.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hmgene/mudcookies/HEAD/src/seurat-merge-cluster-marker.sh -------------------------------------------------------------------------------- /src/seurat-postanalysis.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hmgene/mudcookies/HEAD/src/seurat-postanalysis.r -------------------------------------------------------------------------------- /src/sftp.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hmgene/mudcookies/HEAD/src/sftp.sh -------------------------------------------------------------------------------- /src/sierra.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hmgene/mudcookies/HEAD/src/sierra.sh -------------------------------------------------------------------------------- /src/singler.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hmgene/mudcookies/HEAD/src/singler.r -------------------------------------------------------------------------------- /src/singularity.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hmgene/mudcookies/HEAD/src/singularity.sh -------------------------------------------------------------------------------- /src/slingshot.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hmgene/mudcookies/HEAD/src/slingshot.r -------------------------------------------------------------------------------- /src/slurm-examples.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hmgene/mudcookies/HEAD/src/slurm-examples.sh -------------------------------------------------------------------------------- /src/train-celltype-with-scpred.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hmgene/mudcookies/HEAD/src/train-celltype-with-scpred.sh -------------------------------------------------------------------------------- /src/wsl.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hmgene/mudcookies/HEAD/src/wsl.sh -------------------------------------------------------------------------------- /test/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hmgene/mudcookies/HEAD/test/README.md -------------------------------------------------------------------------------- /test/Screen Shot 2020-12-19 at 5.07.40 PM.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hmgene/mudcookies/HEAD/test/Screen Shot 2020-12-19 at 5.07.40 PM.png -------------------------------------------------------------------------------- /test/Screen Shot 2020-12-19 at 8.34.18 PM.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hmgene/mudcookies/HEAD/test/Screen Shot 2020-12-19 at 8.34.18 PM.png -------------------------------------------------------------------------------- /test/pbmc_1.harmony.diff.clusters: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hmgene/mudcookies/HEAD/test/pbmc_1.harmony.diff.clusters -------------------------------------------------------------------------------- /test/pbmc_1.harmony.diff.csv.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hmgene/mudcookies/HEAD/test/pbmc_1.harmony.diff.csv.csv -------------------------------------------------------------------------------- /test/pbmc_1.harmony.diff.csv.rcmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hmgene/mudcookies/HEAD/test/pbmc_1.harmony.diff.csv.rcmd -------------------------------------------------------------------------------- /test/pbmc_1.harmony.rds.rcmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hmgene/mudcookies/HEAD/test/pbmc_1.harmony.rds.rcmd -------------------------------------------------------------------------------- /test/pbmc_1.harmony_cluster.rds.rcmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hmgene/mudcookies/HEAD/test/pbmc_1.harmony_cluster.rds.rcmd -------------------------------------------------------------------------------- /test/pbmc_1.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hmgene/mudcookies/HEAD/test/pbmc_1.rda -------------------------------------------------------------------------------- /test/pbmc_1.scpred.rds.rcmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hmgene/mudcookies/HEAD/test/pbmc_1.scpred.rds.rcmd -------------------------------------------------------------------------------- /test/pbmc_2.predict.rds.rcmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hmgene/mudcookies/HEAD/test/pbmc_2.predict.rds.rcmd -------------------------------------------------------------------------------- /test/pbmc_2.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hmgene/mudcookies/HEAD/test/pbmc_2.rda -------------------------------------------------------------------------------- /test/test-harmony.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | echo "test harmony" 4 | --------------------------------------------------------------------------------