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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.

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lincsilincsdrug repurposingdrug discoverytranscriptomicsgene expressiongene knockdowngene overexpressionchemical perturbagendrugfindrbioinformaticsbioinformatics-pipeline

7.26 score 13 stars 164 scripts 209 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.

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kinasephosphatasespamchipkinomerandom samplingpermutation analysis

3.78 score 4 stars 76 scripts

creedenzymatic - creedenzymatic

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

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bioconductorbioconductor-packagekinome

3.46 score 1 stars 29 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.

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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.

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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