├── .gitignore ├── APA ├── README.md ├── Snakefile.smk ├── bin │ ├── Dapars2_Multi_Sample.py │ └── test.py ├── config.yaml ├── fq │ ├── B_1_R1.fq.gz │ ├── B_1_R2.fq.gz │ ├── B_2_R1.fq.gz │ ├── B_2_R2.fq.gz │ ├── CD4_1_R1.fq.gz │ ├── CD4_1_R2.fq.gz │ ├── CD4_2_R1.fq.gz │ ├── CD4_2_R2.fq.gz │ ├── CD8_1_R1.fq.gz │ ├── CD8_1_R2.fq.gz │ ├── CD8_2_R1.fq.gz │ ├── CD8_2_R2.fq.gz │ ├── CLP_1_R1.fq.gz │ ├── CLP_1_R2.fq.gz │ ├── CLP_2_R1.fq.gz │ ├── CLP_2_R2.fq.gz │ ├── CMP_1_R1.fq.gz │ ├── CMP_1_R2.fq.gz │ ├── CMP_2_R1.fq.gz │ ├── CMP_2_R2.fq.gz │ ├── EryA_1_R1.fq.gz │ ├── EryA_1_R2.fq.gz │ ├── EryA_2_R1.fq.gz │ ├── EryA_2_R2.fq.gz │ ├── EryB_1_R1.fq.gz │ ├── EryB_1_R2.fq.gz │ ├── EryB_2_R1.fq.gz │ ├── EryB_2_R2.fq.gz │ ├── GMP_1_R1.fq.gz │ ├── GMP_1_R2.fq.gz │ ├── GMP_2_R1.fq.gz │ ├── GMP_2_R2.fq.gz │ ├── Gn_1_R1.fq.gz │ ├── Gn_1_R2.fq.gz │ ├── Gn_2_R1.fq.gz │ ├── Gn_2_R2.fq.gz │ ├── LT-HSC_1_R1.fq.gz │ ├── LT-HSC_1_R2.fq.gz │ ├── LT-HSC_2_R1.fq.gz │ ├── LT-HSC_2_R2.fq.gz │ ├── MEP_1_R1.fq.gz │ ├── MEP_1_R2.fq.gz │ ├── MEP_2_R1.fq.gz │ ├── MEP_2_R2.fq.gz │ ├── MK_1_R1.fq.gz │ ├── MK_1_R2.fq.gz │ ├── MK_2_R1.fq.gz │ ├── MK_2_R2.fq.gz │ ├── MPP_1_R1.fq.gz │ ├── MPP_1_R2.fq.gz │ ├── MPP_2_R1.fq.gz │ ├── MPP_2_R2.fq.gz │ ├── Mo_1_R1.fq.gz │ ├── Mo_1_R2.fq.gz │ ├── Mo_2_R1.fq.gz │ ├── Mo_2_R2.fq.gz │ ├── Mp_1_R1.fq.gz │ ├── Mp_1_R2.fq.gz │ ├── Mp_2_R1.fq.gz │ ├── Mp_2_R2.fq.gz │ ├── NK_1_R1.fq.gz │ ├── NK_1_R2.fq.gz │ ├── NK_2_R1.fq.gz │ ├── NK_2_R2.fq.gz │ ├── ST-HSC_1_R1.fq.gz │ ├── ST-HSC_1_R2.fq.gz │ ├── ST-HSC_2_R1.fq.gz │ └── ST-HSC_2_R2.fq.gz ├── meta.tsv └── rule │ ├── QC │ ├── FastQC.rule │ └── multiqc.rule │ ├── TAPAS │ └── tapas.rule │ ├── alignment │ └── align.rule │ ├── dapars │ └── run.rule │ ├── mountainClimber │ └── run.rule │ └── qapa │ └── run.rule ├── AlternativeSplice ├── README.md ├── Snakefile.smk ├── config.yaml ├── example_data │ └── FASTQ │ │ ├── T122_V2TC_T_2M_b1_r1.fq.gz │ │ ├── T122_V2TC_T_2M_b1_r2.fq.gz │ │ ├── T123_V2TC_T_2M_b1_r1.fq.gz │ │ ├── T123_V2TC_T_2M_b1_r2.fq.gz │ │ ├── T124_V2TC_T_2M_b1_r1.fq.gz │ │ ├── T124_V2TC_T_2M_b1_r2.fq.gz │ │ ├── T37_TNP_T_1M_b1_r1.fq.gz │ │ ├── T37_TNP_T_1M_b1_r2.fq.gz │ │ ├── T46_TNP_T_1M_b1_r1.fq.gz │ │ ├── T46_TNP_T_1M_b1_r2.fq.gz │ │ ├── T6_V2TC_T_1M_b1_r1.fq.gz │ │ ├── T6_V2TC_T_1M_b1_r2.fq.gz │ │ ├── T7_V2TC_T_1M_b1_r1.fq.gz │ │ ├── T7_V2TC_T_1M_b1_r2.fq.gz │ │ ├── T88_TNP_T_2M_b1_r1.fq.gz │ │ ├── T88_TNP_T_2M_b1_r2.fq.gz │ │ ├── T89_TNP_T_2M_b1_r1.fq.gz │ │ ├── T89_TNP_T_2M_b1_r2.fq.gz │ │ ├── T93_TNP_T_2M_b1_r1.fq.gz │ │ ├── T93_TNP_T_2M_b1_r2.fq.gz │ │ ├── WXF100_TNP_T_EM_b1_r1.fq.gz │ │ ├── WXF100_TNP_T_EM_b1_r2.fq.gz │ │ ├── WXF121_V2TC_T_EM_b1_r1.fq.gz │ │ ├── WXF121_V2TC_T_EM_b1_r2.fq.gz │ │ ├── WXF144_V2TC_T_EM_b1_r1.fq.gz │ │ ├── WXF144_V2TC_T_EM_b1_r2.fq.gz │ │ ├── WXF150_V2TC_T_EM_b1_r1.fq.gz │ │ ├── WXF150_V2TC_T_EM_b1_r2.fq.gz │ │ ├── WXF48_TNP_T_EM_b1_r1.fq.gz │ │ ├── WXF48_TNP_T_EM_b1_r2.fq.gz │ │ ├── WXF49_TNP_T_EM_b1_r1.fq.gz │ │ ├── WXF49_TNP_T_EM_b1_r2.fq.gz │ │ ├── WXF50_TNP_T_EM_b1_r1.fq.gz │ │ ├── WXF50_TNP_T_EM_b1_r2.fq.gz │ │ ├── WXF83_TNP_T_EM_b1_r1.fq.gz │ │ ├── WXF83_TNP_T_EM_b1_r2.fq.gz │ │ ├── WXF94_TNP_T_EM_b1_r1.fq.gz │ │ ├── WXF94_TNP_T_EM_b1_r2.fq.gz │ │ ├── WXF96_TNP_T_EM_b1_r1.fq.gz │ │ ├── WXF96_TNP_T_EM_b1_r2.fq.gz │ │ ├── hNPC_TNP_P15_b1_r1.fq.gz │ │ ├── hNPC_TNP_P15_b1_r2.fq.gz │ │ ├── hNPC_V2TC_P14_b1_r1.fq.gz │ │ ├── hNPC_V2TC_P14_b1_r2.fq.gz │ │ ├── hNPC_WT_P12_b1_r1.fq.gz │ │ └── hNPC_WT_P12_b1_r2.fq.gz ├── meta.tsv ├── rule │ ├── QC │ │ ├── FastQC.rule │ │ ├── GeneBodyQC.rule │ │ └── MultiQC.rule │ ├── alignment │ │ └── STAR_PE.rule │ └── quant │ │ ├── DEXseq_count.rule │ │ ├── ExonPart_cal.rule │ │ ├── GeneCounts.rule │ │ ├── RSEM.rule │ │ ├── qapa.rule │ │ └── rMATs.rule └── script │ ├── Exon_Part.sh │ ├── GeneCounts.R │ ├── RSEM_extract.R │ ├── StarGeneCounts.R │ ├── dexseq_count.py │ ├── dexseq_prepare_annotation.py │ ├── filter_SJs.R │ ├── make_coding_gtf.R │ └── mergePSI.R ├── DNASeq ├── WES │ ├── README.md │ ├── Snakefile.smk │ ├── bin │ │ └── makeGistic.R │ ├── config.yaml │ ├── fq │ │ ├── PDAC_001_C.r1.fq.gz │ │ ├── PDAC_001_C.r2.fq.gz │ │ ├── PDAC_001_N.r1.fq.gz │ │ ├── PDAC_001_N.r2.fq.gz │ │ ├── PDAC_001_P.r1.fq.gz │ │ ├── PDAC_001_P.r2.fq.gz │ │ ├── PDAC_002_T.r1.fq.gz │ │ ├── PDAC_002_T.r2.fq.gz │ │ ├── PDAC_003_C.r1.fq.gz │ │ ├── PDAC_003_C.r2.fq.gz │ │ ├── PDAC_003_N.r1.fq.gz │ │ ├── PDAC_003_N.r2.fq.gz │ │ ├── PDAC_004_C.r1.fq.gz │ │ ├── PDAC_004_C.r2.fq.gz │ │ ├── PDAC_004_N.r1.fq.gz │ │ ├── PDAC_004_N.r2.fq.gz │ │ ├── PDAC_004_P.r1.fq.gz │ │ ├── PDAC_004_P.r2.fq.gz │ │ ├── PDAC_004_T.r1.fq.gz │ │ ├── PDAC_004_T.r2.fq.gz │ │ ├── PDAC_005_C.r1.fq.gz │ │ ├── PDAC_005_C.r2.fq.gz │ │ ├── PDAC_005_P.r1.fq.gz │ │ ├── PDAC_005_P.r2.fq.gz │ │ ├── PDAC_006_C.r1.fq.gz │ │ ├── PDAC_006_C.r2.fq.gz │ │ ├── PDAC_007_C.r1.fq.gz │ │ ├── PDAC_007_C.r2.fq.gz │ │ ├── PDAC_007_P.r1.fq.gz │ │ ├── PDAC_007_P.r2.fq.gz │ │ ├── PDAC_008_C.r1.fq.gz │ │ ├── PDAC_008_C.r2.fq.gz │ │ ├── PDAC_008_N.r1.fq.gz │ │ ├── PDAC_008_N.r2.fq.gz │ │ ├── PDAC_008_P.r1.fq.gz │ │ ├── PDAC_008_P.r2.fq.gz │ │ ├── PDAC_009_C.r1.fq.gz │ │ ├── PDAC_009_C.r2.fq.gz │ │ ├── PDAC_009_N.r1.fq.gz │ │ ├── PDAC_009_N.r2.fq.gz │ │ ├── PDAC_010_C.r1.fq.gz │ │ ├── PDAC_010_C.r2.fq.gz │ │ ├── PDAC_010_N.r1.fq.gz │ │ ├── PDAC_010_N.r2.fq.gz │ │ ├── PDAC_012_P.r1.fq.gz │ │ ├── PDAC_012_P.r2.fq.gz │ │ ├── PDAC_016_C.r1.fq.gz │ │ ├── PDAC_016_C.r2.fq.gz │ │ ├── PDAC_016_N.r1.fq.gz │ │ ├── PDAC_016_N.r2.fq.gz │ │ ├── PDAC_016_P.r1.fq.gz │ │ └── PDAC_016_P.r2.fq.gz │ ├── meta.csv │ └── rule │ │ ├── Alignment │ │ └── BWA.rule │ │ ├── BamProc │ │ ├── BQSR.rule │ │ ├── MergeAndMark.rule │ │ └── VQSR.rule │ │ ├── Maf.Rmd │ │ ├── Mutect2 │ │ └── mutect.rule │ │ └── QC │ │ ├── FastQC.rule │ │ ├── GeneBodyQC.rule │ │ └── MultiQC.rule └── WGS │ ├── README.md │ ├── Snakefile.smk │ ├── config.yaml │ ├── fq │ ├── ET5_MEP.DHG16955_S_BHCLWVCCXY.L6.R1.fq.gz │ ├── ET5_MEP.DHG16955_S_BHCLWVCCXY.L6.R2.fq.gz │ ├── ET5_MEP.DHG16955_S_BHCLWVCCXY.L7.R1.fq.gz │ ├── ET5_MEP.DHG16955_S_BHCLWVCCXY.L7.R2.fq.gz │ ├── ET5_MEP.DHG16955_S_BHCLWVCCXY.L8.R1.fq.gz │ └── ET5_MEP.DHG16955_S_BHCLWVCCXY.L8.R2.fq.gz │ ├── meta.csv │ └── rule │ ├── BamProc │ ├── BQSR.rule │ ├── MergeAndMark.rule │ └── VQSR.rule │ ├── QC │ ├── FastQC.rule │ ├── GeneBodyQC.rule │ └── MultiQC.rule │ └── alignment │ └── BWA.rule ├── DropSeq └── snakefile.smk ├── DropSeq_processing ├── README.md ├── Snakefile.smk ├── config.yaml ├── example_data │ ├── CB │ │ ├── Adult-Adipose1.tsv │ │ └── Adult-Liver1.tsv │ └── FASTQ │ │ ├── Adult-Adipose1_R1.fastq.gz │ │ ├── Adult-Adipose1_R2.fastq.gz │ │ ├── Adult-Liver1_R1.fastq.gz │ │ └── Adult-Liver1_R2.fastq.gz ├── meta.tsv ├── rule │ ├── QC │ │ ├── FastQC.rule │ │ └── MultiQC.rule │ ├── alignment │ │ └── alignment.rule │ ├── apa │ │ └── scape.rule │ └── pre_process │ │ └── process_fq.rule └── script │ └── manibam.py ├── NCBI_sra ├── README.md ├── Snakefile.smk ├── config.yaml └── meta.tsv ├── README.md ├── RNASeq ├── README.md ├── Snakefile.smk ├── config.yaml ├── example_data │ └── FASTQ │ │ ├── SRR1039508_R1.fastq.gz │ │ ├── SRR1039508_R2.fastq.gz │ │ ├── SRR1039509_R1.fastq.gz │ │ ├── SRR1039509_R2.fastq.gz │ │ ├── SRR1039512_R1.fastq.gz │ │ ├── SRR1039512_R2.fastq.gz │ │ ├── SRR1039513_R1.fastq.gz │ │ └── SRR1039513_R2.fastq.gz ├── meta.tsv ├── rule │ ├── QC │ │ ├── FastQC.rule │ │ ├── GeneBodyQC.rule │ │ └── MultiQC.rule │ ├── alignment │ │ └── STAR_PE.rule │ └── quant │ │ ├── GeneCounts.rule │ │ └── RSEM.rule └── script │ ├── GeneCounts.R │ ├── RSEM_extract.R │ └── StarGeneCounts.R ├── ScientificData ├── README.md ├── final │ ├── Lineage_gene.merge.pdf │ ├── Lineage_gene.pdf │ ├── Lineage_gene.single.pdf │ ├── annotation_distribution.pdf │ ├── cooks_dis.pdf │ ├── distance.pdf │ ├── genebody_cov.pdf │ ├── pca_plot.pdf │ ├── qual_boxplot.pdf │ ├── stage_go.pdf │ ├── stage_kegg.pdf │ ├── stage_specific_gene.pdf │ └── star_df_use.tsv ├── prepare_matrix │ ├── README.md │ ├── bin │ │ ├── collapse.R │ │ ├── fastq.py │ │ └── q30.py │ ├── config.yaml │ ├── meta.tsv │ └── snakefile.smk └── scientific_data.Rmd ├── Spatial ├── README.md ├── config.yaml ├── data │ └── ranger │ │ └── A │ │ ├── barcodes.tsv.gz │ │ ├── possorted_genome_bam.bam │ │ └── possorted_genome_bam.bam.bai ├── fq │ └── A.fastq ├── meta.tsv └── sicelorel_pipe.smk ├── Tools ├── READEM.md └── function_study │ └── shRNA_design.py └── scRNASeq ├── README.md ├── config.yaml ├── fq ├── SRR10919863_1.fastq.gz ├── SRR10919863_2.fastq.gz ├── SRR10919864_1.fastq.gz ├── SRR10919864_2.fastq.gz ├── SRR10919865_1.fastq.gz ├── SRR10919865_2.fastq.gz ├── SRR10919866_1.fastq.gz ├── SRR10919866_2.fastq.gz ├── SRR10919880_1.fastq.gz └── SRR10919880_2.fastq.gz ├── meta.tsv └── snakefile.smk /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zhou-ran/workflows/HEAD/.gitignore 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