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.
Last updated 4 days ago
lincsilincsdrug repurposingdrug discoverytranscriptomicsgene expressiongene knockdowngene overexpressionchemical perturbagendrugfindrbioinformaticsbioinformatics-pipeline
6.13 score 8 stars 145 scriptsenrichR - Provides an R Interface to 'Enrichr'
Provides an R interface to all 'Enrichr' databases. 'Enrichr' is a web-based tool for analysing gene sets and returns any enrichment of common annotated biological features. Quoting from their website 'Enrichment analysis is a computational method for inferring knowledge about an input gene set by comparing it to annotated gene sets representing prior biological knowledge.' See <https://maayanlab.cloud/Enrichr/> for further details.
Last updated 25 days ago
4.87 score 7 dependents 912 scripts 147 downloads
KRSA - KRSA: Kinome Random Sampling Analyzer
The goal of this package is to analyze the PamChip data and identify the changes in the active kinome. The package can preprocess the PamChip data output from BioNavigator and use Random Sampling and Permutation Analysis to identify upstream kinases. Additionally, this package provides a set of useful visualizations for the PamChip data.
Last updated 2 days ago
kinasephosphatasespamchipkinomerandom samplingpermutation analysis
4.32 score 4 stars 48 scriptscreedenzymatic - creedenzymatic
Combine kinome results from KRSA and UKA and other tools A package for integrating upstream kinases analyses
Last updated 9 months ago
bioconductorbioconductor-packagekinome
3.60 score 1 stars 20 scriptsPCSF - Network-based interpretation of highthroughput data
The PCSF package performs an integrated analysis of highthroughput data using the interaction networks as a template, and interprets the biological landscape of interaction networks with respect to the data, which potentially leads to predictions of functional units. It also interactively visualize the resulting subnetwork with functional enrichment analysis.
Last updated 6 years ago
cpp
2.72 score 1 dependents 35 scriptsKinaseTauScore - Tau Scores For Human Kinases
This data package provides the tau scores for each kinase based on its activity in Alzheimer's disease samples. The data was generated by using an siRNA Library to knock down individual kinases and then measuring the total Tau protein Expression and the phopho-Tau protein expression. The resulting data wasc reposited online. This package processes the resulting data to create a meaningful Tau Score for each Kinase based on its activity.
Last updated 3 years ago
experimentdataproteomeexpressiondata
2.70 scoreBioPathNet - BioPathNet: Three Pod Analysis System
This package aims to provide a simple interface to perform the Three Pod Analysis of RNASeq dataaset. In addition, this also provides utility functions to perform the individual components.
Last updated 2 years ago
bioinformaticsbioinformatics-pipelineilincstranscriptomics
2.00 score 2 stars 5 scriptsKINNET - Kinase INteraction NETwork Generation
This package provides the functionality to process PamGene's PamChip Data Output and generate kinase interaction networks from that. This project uses a bayesian algorithm to generate bayesian networks for defining dependence relationships between peptide sequences in the PamChip data. It then uses a novel kinase assignment method to assign upstream kinases to each peptide which is then output as a graph.
Last updated 3 years ago
2.00 score 2 stars 3 scripts
kinograte - Kinograte: Netwrok-based multi-omics Integration
Netwrok-based multi-omics integration using a prize-collecting Steiner forest (PCSF) algorithm.
Last updated 3 years ago
1.70 score 2 scripts