| A. Functional enrichment-based methods |
| Over-Representation Analysis |
gProfiler |
https://biit.cs.ut.ee/gprofiler/gost |
[48] |
| WebGestalt 2019 |
https://www.webgestalt.org/ |
[155] |
| Panther Gene List Analysis |
https://pantherdb.org/ |
[49], [156]
|
| Enrichr |
https://maayanlab.cloud/Enrichr/ |
[50] |
| Gene Set Enrichment Analysis |
WebGestalt 2019 |
https://www.webgestalt.org/ |
[155] |
| EndoDB |
https://vibcancer.be/software-tools/endodb |
[46] |
| EnrichNet |
https://www.enrichnet.org |
[157] |
| ShinyGO |
https://ge-lab.org/go/. |
[158] |
| GeneTrail |
https://genetrail.bioinf.uni-sb.de |
[159] |
| TissueEnrich |
https://tissueenrich.gdcb.iastate.edu/. |
[160] |
| WhichGenes |
https://www.whichgenes.org/api/. |
[161] |
| ClusterGrammer |
https://github.com/maayanlab/clustergrammer |
[162] |
| Gene Set Variation Analysis |
PAGER Web APP |
https://aimed-lab.shinyapps.io/PAGERwebapp/ |
[163] |
| B. Cell-cell communication inference |
|
TALKLR |
https://yuliangwang.shinyapps.io/talklr/ |
[164] |
|
InterCellar |
https://bioconductor.org/packages/InterCellar/ |
[165] |
| Expression-permutation based methods |
scConnect |
https://github.com/JonETJakobsson/scConnect |
[166] |
| CellPhoneDB |
https://www.cellphonedb.org/ |
[63] |
| CellLinker |
https://www.rna-society.org/cellinker/ |
[167] |
| FlyPhoneDB |
https://www.flyrnai.org/tools/fly_phone/web/ |
[168] |
| C. Gene regulatory network inference |
| GRN Inference Methods |
DIANE |
https://diane.bpmp.inrae.fr |
[169] |
| COXPRESdb |
https://coxpresdb.jp |
[170] |
| GeneFriends |
https://www.GeneFriends.org |
[171] |
| COEXPEDIA |
https://www.coexpedia.org |
[172] |
| SEEK |
https://seek.princeton.edu/ |
[173] |
|
GeNeCK |
https://lce.biohpc.swmed.edu/geneck |
[174] |
| D. Single-cell metabolic network inference |
Genome-Scale Metabolic
Reconstruction databases
|
Virtual Metabolic Human |
https://www.vmh.life/#home |
[175] |
| Metabolic Atlas |
https://metabolicatlas.org/explore/Human-GEM/gem-browser |
[176] |
| BiGG Models |
https://bigg.ucsd.edu/ |
[177] |
| Flux visualizations |
Fluxer |
https://fluxer.umbc.edu/ |
[178] |
| Escher-FBA |
https://sbrg.github.io/escher-fba/#/ |
[179] |
| E. Unsupervised multi-omics data fusion |
| Bulk multi-omics datasets |
MiBiOmics |
https://shiny-bird.univ-nantes.fr/app/Mibiomics |
[180] |
| OmicsNet |
https://www.omicsnet.ca/OmicsNet/home.xhtml |
[181] |
| F. ML-based Gene Prioritization (single or multiple data sources) |
| ML-Based Gene Prioritization |
ToppGene |
https://toppgene.cchmc.org/prioritization.jsp |
[182] |
| PhenoPred |
https://www.phenopred.org/ |
[183] |
| Endeavour |
https://endeavour.esat.kuleuven.be/ |
[146] |
| pBRIT |
https://143.169.238.105/pbrit/ |
[184] |
| PhenoApt |
https://www.phenoapt.org/ |
[185] |
| Text mining-based Gene Prioritization |
PolySearch2 |
https://polysearch.ca/ |
[186] |
| Network-based Gene Prioritization |
PINTA |
https://securehomes.esat.kuleuven.be/∼bioiuser/pinta/ |
[187] |
| GeneMANIA |
https://genemania.org/ |
[188] |
| WebPropagate |
https://anat.cs.tau.ac.il/WebPropagate/ |
[189] |
