pici/rnaseq repository overview

Program list: Names are links, and execution code is indented.

• samtools⁠

  samtools [args]

• bam-readcount⁠

  bam-readcount [args]

• STAR⁠

  STAR [args]

• HTSeq⁠

  htseq-count [args]

• fastqc⁠

  fastqc [args]

• picard⁠

  java -jar picard-tools-1.140/picard.jar [args]

• flexbar⁠

  flexbar [args]

• kallisto⁠

  kallisto [args]

• Java Oracle 8⁠

  java [args]

• Scala⁠

  scala

• Python⁠ + Numpy⁠ + Scipy⁠ + pandas⁠

  python

• bowtie2⁠

  bowtie2 [args]

• R⁠ + limma⁠ + DESeq2⁠ + edgeR⁠ + sleuth⁠

  R

  library("sleuth")

• Tophat2⁠

  tophat2 [args]

• Cufflinks⁠

  cufflinks [args]

• hisat2⁠

  hisat2 [args]

• sortmerna⁠

  sortmerna [args]

• trimmomatic⁠

  java -jar trimmomatic/trimmomatic.jar [args]

• samstat⁠

  samstat [args]

• RSeqC⁠

  python RSeqC/<file_name.py> [args]