R-universe search: recount2

Showing 3 of total 3 results (show query)

bioc

psichomics:Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation

Interactive R package with an intuitive Shiny-based graphical interface for alternative splicing quantification and integrative analyses of alternative splicing and gene expression based on The Cancer Genome Atlas (TCGA), the Genotype-Tissue Expression project (GTEx), Sequence Read Archive (SRA) and user-provided data. The tool interactively performs survival, dimensionality reduction and median- and variance-based differential splicing and gene expression analyses that benefit from the incorporation of clinical and molecular sample-associated features (such as tumour stage or survival). Interactive visual access to genomic mapping and functional annotation of selected alternative splicing events is also included.

Maintained by Nuno Saraiva-Agostinho. Last updated 5 months ago.

sequencing rnaseq alternativesplicing differentialsplicing transcription gui principalcomponent survival biomedicalinformatics transcriptomics immunooncology visualization multiplecomparison geneexpression differentialexpression alternative-splicing bioconductor data-analyses differential-gene-expression differential-splicing-analysis gene-expression gtex recount2 rna-seq-data splicing-quantification sra tcga vast-tools cpp

12.8 match 36 stars 6.95 score 31 scripts

bioc

megadepth:megadepth: BigWig and BAM related utilities

This package provides an R interface to Megadepth by Christopher Wilks available at https://github.com/ChristopherWilks/megadepth. It is particularly useful for computing the coverage of a set of genomic regions across bigWig or BAM files. With this package, you can build base-pair coverage matrices for regions or annotations of your choice from BigWig files. Megadepth was used to create the raw files provided by https://bioconductor.org/packages/recount3.

Maintained by David Zhang. Last updated 3 months ago.

software coverage dataimport transcriptomics rnaseq preprocessing bam bigwig daspter megadepth recount2 recount3

11.0 match 12 stars 6.69 score 7 scripts 3 dependents

bioc

TCGAbiolinks:TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data

The aim of TCGAbiolinks is : i) facilitate the GDC open-access data retrieval, ii) prepare the data using the appropriate pre-processing strategies, iii) provide the means to carry out different standard analyses and iv) to easily reproduce earlier research results. In more detail, the package provides multiple methods for analysis (e.g., differential expression analysis, identifying differentially methylated regions) and methods for visualization (e.g., survival plots, volcano plots, starburst plots) in order to easily develop complete analysis pipelines.

Maintained by Tiago Chedraoui Silva. Last updated 26 days ago.

dnamethylation differentialmethylation generegulation geneexpression methylationarray differentialexpression pathways network sequencing survival software bioc bioconductor gdc integrative-analysis tcga tcga-data tcgabiolinks

2.9 match 305 stars 14.45 score 1.6k scripts 6 dependents