Pathway和network分析是生物信息下游数据分析中相当重要的一个环节，偶然看到一个2015年的一片文章汇总了当下所有的分析方法和工具，分享给大家：
| 软件名称 | 算法 | 平台 | 数据 | 网址 |
| g:Profiler | ORA+FET (modified for ordered gene lists) | WT, RP | GL | http://biit.cs.ut.ee/gprofiler |
| CAMERA | ORA+FET (corrected for gene correlation) | RP | GL, EXP | http://www.bioconductor.org/packages/releas e/bioc/html/limma.html |
| GO | DB | WT, DS | NA | http://geneontology.org |
| GSEA, ssGSEA | FCS+KS | DS, CL, RP | GLV | http://www.broadinstitute.org/gsea |
| GSVA | FCS+KS | RP | GLV | http://www.bioconductor.org/packages/releas e/bioc/html/GSVA.html |
| HumanCyc | DB | WT | NA | http://humancyc.org |
| KEGG | DB | WT, DS | NA | http://www.genome.jp/kegg/pathway.html |
| REACTOME | DB | WT, DS | NA | http://www.reactome.org |
| SLEA | FCS+Z | DS, CL | GLV | http://bg.upf.edu/slea |
| Babelomics | ORA, FCS+FET | WT | GL | http://www.babelomics.org |
| BiNGO | ORA+HT | CP | GL | http://www.psb.ugent.be/cbd/papers/BiNGO |
| ConceptGen | ORA+FET | WT | GL | http://conceptgen.ncibi.org |
| Gitools | ORA+FET, FCS+Z | DS, CL | GL,GLV | http://www.gitools.org |
| GoMiner | ORA+FET | WT | GL | http://discover.nci.nih.gov/gominer |
| GOstats | ORA+HT | RP | GL | http://www.bioconductor.org/packages/releas e/bioc/html/GOstats.html |
| iPAGE | ORA+MI | DS, CL, WT | GL | https://tavazoielab.c2b2.columbia.edu/iPAGE |
| ToppGene | ORA | WT | GL | http://toppgene.cchmc.org |
| BioGRID | DB | WT, DS | NA | http://thebiogrid.org |
| EnrichNet | RWR | DS, WT, CP | GL | http://www.enrichnet.org |
| GeneMANIA | DB, RR | CP, WT | GL | http://www.genemania.org |
| Hypermodules | GS+CC | CL,CP | GL, CD | http://apps.cytoscape.org/apps/hypermodules |
| INTACT | DB | WT,DS | NA | http://www.ebi.ac.uk/intact |
| iRefIndex | DB | DS | NA | http://irefindex.org/wiki/index.php |
| MEMo | ME | CL, DS | SSM, SNA | http://cbio.mskcc.org/tools/memo |
| NetBox | EB | CL, DS | GL | http://cbio.mskcc.org/tools/netbox |
| ReactomeFIViz | GC, FG, MCL | CP | GL, GLV | http://apps.cytoscape.org/apps/reactomefiplu gin |
| ResponseNet | MCFL | CP, WT | GLV (gene weights) | http://bioinfo.bgu.ac.il/respnet |
| STRING | DB | WT, DS | NA | http://string-db.org |
| Dendrix | ME | CP, DS, WT | SM | http://compbio.cs.brown.edu/projects/dendrix |
| iCluster+ | GLV | RP | SSM, SNA, EXP | http://www.mskcc.org/research/epidemiology- biostatistics/biostatistics/iclusterplus |
| Pathifier | PDS | CL, RP | EXP | http://www.weizmann.ac.il/complex/compphy s/software/yotam/pathifier |
| SIRENE | BC | ML | EXP | http://cbio.ensmp.fr/sirene |
| HotNet | UD | ML | GLV | http://compbio.cs.brown.edu/projects/hotnet |
| TieDIE | UD | CL, ML | SSM, SCNA, EXP | https://sysbiowiki.soe.ucsc.edu/tiedie |
| SPIA | RW | RP | EXP | http://www.bioconductor.org/packages/devel/ bioc/html/SPIA.html |
| ARACNE | DPI | CL, DS, RP | EXP | http://wiki.c2b2.columbia.edu/califanolab/inde x.php/Software/ARACNE |
| GENIE3 | LR | ML, RC | EXP | http://homepages.inf.ed.ac.uk/vhuynht/softwa re.html |
| PARADIGM | PGM | WT, DS, CL | SSM, SCNA, EXP, METH | http://paradigm.five3genomics.com |
| PARADIGM- Shift | PGM | DS | SSM, SCNA, EXP, METH | http:github.org/sng87/paradigmshift |
| PathOlogist | PGM | CL, ML | EXP | ftp://ftp1.nci.nih.gov/pub/pathologist |
| DataRail | BKRM | DS, RP, CP | EXP+ PD | https://code.google.com/p/sbpipeline/wiki/Dat aRail |
| PSA | NF | CA | EXP, CHIP | http://apps.cytoscape.org/apps/pathwayscori ngapplication |
| NetPhorest | NF | WT | GL | http://netphorest.info |
| NetworKIN | NF | WT | GL | http://networkin.info |
| CellNet- Optimizer | BKRM | DS, RP, CP | EXP+P D | http://www.cellnopt.org |
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参考资料：
1. Creixell P, Reimand J, Haider S, et al. Pathway and network analysis of cancer genomes. Nat Methods. 2015;12(7):615-621.
2.https://pubmed.ncbi.nlm.nih.gov/26125594/
