From: CSA: a web service for the complete process of ChIP-Seq analysis
Platform | system | installation | Interface | Functions & tools | |||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
workflow | Mapping | Quality control | Peak calling | Format convert | Data visualization | Find motifs | GO analysis | Peaks annotation | Pathway analysis | ||||
HOMER[22] | UNIX LINUX MacOS | Perl installation scripts | Command line | – | – | makeTagDirectory | findPeaks | pos2bed.pl,bed2pos.pl | – | findMotifsGenome.pl | annotatePeaks.pl | annotatePeaks.pl | – |
ChIPSeqWorkflow[27] | UNIX LINUX | compilation from source installer | Command line | – | bowtie | – | MACS | Samtools,Bedtools | – | MEME | – | – | GAGE |
ChIPseeker[23] | UNIX LINUX | R package manager | GUI/Command line | √ | – | ChIPseeqerReadCountDistribution | ChIPseeqer | – | peaks coverage | ChIPseeqerFIRE,ChIPseeqerMotifMatch | – | ChIPseeqerAnnotate | iPAGE |
CisGenome[28] | no limitation | compilation from source installer (for Windows) | GUI/command line | – | – | – | tilemapv2 | file_bed2cod,fasta_soft2hardmask, etc. | – | motifmap_matrixscan_genome,etc. | refgene_getnearestgene | – | – |
ChIP-Seq tool[29] | no limitation/UNIX LINUX | not needed | Web server/Command line | – | Chipcor,Chipextract,chipscore | – | Chippeak, chippart | Compactsga,featreplace, etc. | – | – | – | – | – |
Nebula[24] | no limitation | not needed | Web server | √ | Bowtie | FASTQC | HMCan,MICSA,MACS,PeakSplitter,CCAT,FindPeaks | Samtools,Bamtools | – | ChIPmunk,AhoPro | Get peak distribution around TSS/histone | √ | – |
ChIPseek[25] | no limitation | not needed | Web server | – | – | – | HOMER | BEDTools | peak location distribution | HOMER | √ | – | KEGG |
CSA | no limitation | not needed/compilation from script | Web server/local web server | √ | BWA, Bowtie, Bowtie2, SOAP,BLAST,Subread,NGM | deepTools | MACS,MACS2,PeakSeq,PeakRanger,SICER, PePr,BCP,diffReps,SISSRs, FindPeaks, AREM, Fseq, BroadPeak | Samtools, bamCoverage | Mapping results,peak calling results,motif finding, Go annotation,pathway analysis | findMotifsGenome.pl | annotatePeaks.pl | annotatePeaks.pl | iPAGE |