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Table 1 Analysis tools used in this study

From: Empirical assessment of analysis workflows for differential expression analysis of human samples using RNA-Seq

Read aligner RA code Expression modeler EM code Differential expression DE code
Bowtie2 Bw BitSeq Bs Ballgown Bl
HISAT2 Hs cufflinks Cu BitSeq Bs
Kallisto Ka htseq Ht baySeq By
Salmon-FMD Sf IsoEM Ie cuffdiff Cd
Sailfish Sl kallisto Ka DESeq2 De
SeqMap Sm RSEM Rm EBseq Eb
Salmon-Quasi Sq rSeq Rs edgeR Er
STAR Sr Sailfish Sl limma + voom Lo
TopHat2 Th Salmon Sn limma + vst Lv
   STAR Sr NBPseq Nb
   Stringtie St NOISeqBIO No
   eXpress Xs SAMseq Sa
     Sleuth Su
  1. Abbreviations specified in the table are used throughout the figures. Additional details are available in Additional file 1