├── .DS_Store ├── .Rhistory ├── .github └── FUNDING.yml ├── .gitignore ├── .ipynb_checkpoints ├── MakeCountTable_Illumina_SRR-checkpoint.sh ├── MakeCountTable_Illumina_trimgalore_SRR-checkpoint.sh ├── MakeCountTable_Ion_SRR-checkpoint.sh ├── MakeCountTable_Ion_fastq-checkpoint.sh ├── README-checkpoint.md ├── bash-checkpoint.ipynb ├── quantmerge_gene-checkpoint.R ├── quantmerge_gene-checkpoint.ipynb ├── tpTregTconv_rnaseq_experiment_table-checkpoint.csv ├── tximport_R-checkpoint.R └── tximport_R-checkpoint.ipynb ├── LICENSE ├── README.md ├── README_ja.md ├── adapters ├── NexteraPE-PE.fa ├── TruSeq2-PE.fa ├── TruSeq2-SE.fa ├── TruSeq3-PE-2.fa ├── TruSeq3-PE.fa └── TruSeq3-SE.fa ├── bash.ipynb ├── basicrnaseq_se.cwl ├── cwl_tools ├── salmon-index.cwl ├── salmon-quant.cwl └── trim_galore_PE.cwl ├── ikra ├── ikra.sh ├── ikra_Ion_SRR.sh ├── ikra_Ion_fastq.sh ├── img ├── .DS_Store ├── Illumina_PE_fastq_csv.png ├── Illumina_PE_test_output.png ├── docker_mac0.png ├── docker_mac1.png ├── ikra.png ├── ikra_pipeline.drawio ├── ikra_pipeline.png └── salmon1.jpg ├── legacy └── MakeCountTable_Illumina_SRR.sh ├── quantmerge_gene.R ├── quantmerge_gene.ipynb ├── test ├── .DS_Store ├── .ipynb_checkpoints │ └── quantmerge_gene-checkpoint.R ├── Illumina_PE │ ├── Illumina_PE_SRR.csv │ └── Illumina_PE_fastq.csv ├── Illumina_SE │ ├── Illumina_SE_SRR.csv │ └── Illumina_SE_fastq.csv ├── Ion │ ├── Ion_SRR.csv │ └── Ion_fastq.csv ├── cwl_PE │ └── test.sh ├── quantmerge │ └── salmon_output_test_test │ │ └── quant.sf ├── test.full.sh └── test.sh ├── tximport_R.R └── tximport_R.ipynb /.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yyoshiaki/ikra/HEAD/.DS_Store -------------------------------------------------------------------------------- /.Rhistory: -------------------------------------------------------------------------------- 1 | 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