Showing 5 of total 5 results (show query)
bioc
cTRAP:Identification of candidate causal perturbations from differential gene expression data
Compare differential gene expression results with those from known cellular perturbations (such as gene knock-down, overexpression or small molecules) derived from the Connectivity Map. Such analyses allow not only to infer the molecular causes of the observed difference in gene expression but also to identify small molecules that could drive or revert specific transcriptomic alterations.
Maintained by Nuno Saraiva-Agostinho. Last updated 5 months ago.
differentialexpressiongeneexpressionrnaseqtranscriptomicspathwaysimmunooncologygenesetenrichmentbioconductorbioinformaticscmapgene-expressionl1000
11.0 match 5 stars 5.08 score 16 scripts
cogdisreslab
drugfindR:Investigate iLINCS for candidate repurposable drugs
This package provides a convenient way to access the LINCS Signatures available in the iLINCS database. These signatures include Consensus Gene Knockdown Signatures, Gene Overexpression signatures and Chemical Perturbagen Signatures. It also provides a way to enter your own transcriptomic signatures and identify concordant and discordant signatures in the LINCS database.
Maintained by Ali Sajid Imami. Last updated 20 days ago.
lincsilincsdrug repurposingdrug discoverytranscriptomicsgene expressiongene knockdowngene overexpressionchemical perturbagendrugfindrbioinformaticsbioinformatics-pipeline
5.3 match 8 stars 6.16 score 145 scriptsbioc
BayesKnockdown:BayesKnockdown: Posterior Probabilities for Edges from Knockdown Data
A simple, fast Bayesian method for computing posterior probabilities for relationships between a single predictor variable and multiple potential outcome variables, incorporating prior probabilities of relationships. In the context of knockdown experiments, the predictor variable is the knocked-down gene, while the other genes are potential targets. Can also be used for differential expression/2-class data.
Maintained by William Chad Young. Last updated 5 months ago.
networkinferencegeneexpressiongenetargetnetworkbayesian
3.6 match 3.30 score 1 scripts
dosorio
retriever:Generate Disease-Specific Response Signatures from the LINCS-L1000 Data
Generates disease-specific drug-response profiles that are independent of time, concentration, and cell-line. Based on the cell lines used as surrogates, the returned profiles represent the unique transcriptional changes induced by a compound in a given disease.
Maintained by Daniel Osorio. Last updated 3 years ago.
2.8 match 2.26 score 12 scripts
