R-universe search: topic:gene expression

Showing 5 of total 5 results (show query)

bioc

GWENA:Pipeline for augmented co-expression analysis

The development of high-throughput sequencing led to increased use of co-expression analysis to go beyong single feature (i.e. gene) focus. We propose GWENA (Gene Whole co-Expression Network Analysis) , a tool designed to perform gene co-expression network analysis and explore the results in a single pipeline. It includes functional enrichment of modules of co-expressed genes, phenotypcal association, topological analysis and comparison of networks configuration between conditions.

Maintained by Gwenaëlle Lemoine. Last updated 5 months ago.

software geneexpression network clustering graphandnetwork genesetenrichment pathways visualization rnaseq transcriptomics mrnamicroarray microarray networkenrichment sequencing go co-expression enrichment-analysis gene network-analysis pipeline

22.0 match 24 stars 5.76 score 12 scripts

bioc

canceR:A Graphical User Interface for accessing and modeling the Cancer Genomics Data of MSKCC

The package is user friendly interface based on the cgdsr and other modeling packages to explore, compare, and analyse all available Cancer Data (Clinical data, Gene Mutation, Gene Methylation, Gene Expression, Protein Phosphorylation, Copy Number Alteration) hosted by the Computational Biology Center at Memorial-Sloan-Kettering Cancer Center (MSKCC).

Maintained by Karim Mezhoud. Last updated 5 months ago.

gui geneexpression clustering go genesetenrichment kegg multiplecomparison cancer cancer-data gene gene-expression gene-methylation gene-mutation gene-sets methylation mskcc mutations tcltk

19.8 match 7 stars 5.08 score 17 scripts

bioc

recount:Explore and download data from the recount project

Explore and download data from the recount project available at https://jhubiostatistics.shinyapps.io/recount/. Using the recount package you can download RangedSummarizedExperiment objects at the gene, exon or exon-exon junctions level, the raw counts, the phenotype metadata used, the urls to the sample coverage bigWig files or the mean coverage bigWig file for a particular study. The RangedSummarizedExperiment objects can be used by different packages for performing differential expression analysis. Using http://bioconductor.org/packages/derfinder you can perform annotation-agnostic differential expression analyses with the data from the recount project as described at http://www.nature.com/nbt/journal/v35/n4/full/nbt.3838.html.

Maintained by Leonardo Collado-Torres. Last updated 4 months ago.

coverage differentialexpression geneexpression rnaseq sequencing software dataimport immunooncology annotation-agnostic bioconductor count derfinder deseq2 exon gene human illumina junction recount

3.8 match 41 stars 9.57 score 498 scripts 3 dependents

bioc

BioCor:Functional similarities

Calculates functional similarities based on the pathways described on KEGG and REACTOME or in gene sets. These similarities can be calculated for pathways or gene sets, genes, or clusters and combined with other similarities. They can be used to improve networks, gene selection, testing relationships...

Maintained by Lluís Revilla Sancho. Last updated 5 months ago.

statisticalmethod clustering geneexpression network pathways networkenrichment systemsbiology bioconductor-packages bioinformatics functional-similarity gene gene-sets pathway-analysis similarity similarity-measurement

3.6 match 14 stars 6.47 score

ganglilab

genekitr:Gene Analysis Toolkit

Provides features for searching, converting, analyzing, plotting, and exporting data effortlessly by inputting feature IDs. Enables easy retrieval of feature information, conversion of ID types, gene enrichment analysis, publication-level figures, group interaction plotting, and result export in one Excel file for seamless sharing and communication.

Maintained by Yunze Liu. Last updated 3 months ago.

enrichment-analysis gene id-converter plotting

1.8 match 56 stars 6.00 score 24 scripts 1 dependents