clean up and tool deprecation
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- README.md 3 additions, 23 deletionsREADME.md
- chipseq_workflow/bowtie2_qc.R 0 additions, 0 deletionschipseq_workflow/bowtie2_qc.R
- common/enrichemt_notes.md 0 additions, 0 deletionscommon/enrichemt_notes.md
- dge_workflow/RnaSeq_Howto.md 0 additions, 3 deletionsdge_workflow/RnaSeq_Howto.md
- dge_workflow/deprecated/cuffdiff_report.R 0 additions, 0 deletionsdge_workflow/deprecated/cuffdiff_report.R
- dge_workflow/deprecated/cuffdiff_report_NoEnr.R 0 additions, 0 deletionsdge_workflow/deprecated/cuffdiff_report_NoEnr.R
- dge_workflow/deprecated/cutadapt_summary.R 0 additions, 0 deletionsdge_workflow/deprecated/cutadapt_summary.R
- dge_workflow/deprecated/dge_master_template.sh 0 additions, 0 deletionsdge_workflow/deprecated/dge_master_template.sh
- dge_workflow/deprecated/star_align.sh 0 additions, 0 deletionsdge_workflow/deprecated/star_align.sh
- dge_workflow/deprecated/topcuff_utils.sh 230 additions, 0 deletionsdge_workflow/deprecated/topcuff_utils.sh
- dge_workflow/deprecated/tophat_qc.R 0 additions, 0 deletionsdge_workflow/deprecated/tophat_qc.R
- dge_workflow/dge_howto.md 13 additions, 0 deletionsdge_workflow/dge_howto.md
- dge_workflow/dge_utils.sh 41 additions, 275 deletionsdge_workflow/dge_utils.sh
- dge_workflow/featcounts_deseq_mf.R 23 additions, 19 deletionsdge_workflow/featcounts_deseq_mf.R
- dge_workflow/todo.txt 0 additions, 21 deletionsdge_workflow/todo.txt
- misc/DEPRECATED 0 additions, 1 deletionmisc/DEPRECATED
- misc/fastqc_summary.R 0 additions, 0 deletionsmisc/fastqc_summary.R
- misc/spin.R 0 additions, 103 deletionsmisc/spin.R
- misc/spin_utils.sh 0 additions, 27 deletionsmisc/spin_utils.sh
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