enrichR - 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

8.07 score 8 dependents 1.9k scripts 8.5k downloads

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

lincsilincsdrug repurposingdrug discoverytranscriptomicsgene expressiongene knockdowngene overexpressionchemical perturbagendrugfindrbioinformaticsbioinformatics-pipeline

7.18 score 10 stars 151 scripts 179 downloads

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

lincsilincsdrug repurposingdrug discoverytranscriptomicsgene expressiongene knockdowngene overexpressionchemical perturbagendrugfindrbioinformaticsbioinformatics-pipeline

7.17 score 10 stars 148 scripts

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

kinasephosphatasespamchipkinomerandom samplingpermutation analysis

3.86 score 4 stars 72 scripts

creedenzymatic - creedenzymatic

Combine kinome results from KRSA and UKA and other tools A package for integrating upstream kinases analyses

Last updated

bioconductorbioconductor-packagekinome

3.45 score 1 stars 28 scripts

PCSF - 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

cpp

3.15 score 1 dependents 94 scripts

PAVER - PAVER: Pathway Analysis Visualization with Embedding Representations

Summary visualization using embedding representations to reveal underlying themes within sets of pathway terms.

Last updated

2.74 score 11 scripts

KinaseTauScore - 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

experimentdataproteomeexpressiondata

2.70 score

BioPathNet - 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

bioinformaticsbioinformatics-pipelineilincstranscriptomics

2.00 score 2 stars 7 scripts

KINNET - 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

2.00 score 2 stars 5 scripts

kinograte - Kinograte: Netwrok-based multi-omics Integration

Netwrok-based multi-omics integration using a prize-collecting Steiner forest (PCSF) algorithm.

Last updated

1.70 score 3 scripts