BiocGenerics | cran | Package Usage

jorainer/ensembldb

This is the ensembldb development repository.

>= 0.15.10 DESCRIPTION

Size: 6.57 MB - Last synced: 4 days ago - Pushed: 21 days ago

ptelomere/RGalaxy

* DESCRIPTION

Size: 601 KB - Last synced: 9 months ago - Pushed: about 9 years ago

jimhester/GenomicRanges 📦

>= 0.11.3 DESCRIPTION

Size: 8.35 MB - Last synced: about 1 year ago - Pushed: about 9 years ago

TRON-Bioinformatics/splice2neo

R package to analyze aberrant splicing junctions in tumor samples to identify neoepitopes

* DESCRIPTION

Size: 11.1 MB - Last synced: about 1 month ago - Pushed: about 1 month ago

rscharpf/VanillaICE-release

>= 0.13.6 DESCRIPTION

Size: 1.24 MB - Last synced: about 1 year ago - Pushed: almost 9 years ago

gexijin/idepGolem

* DESCRIPTION

Size: 5.08 MB - Last synced: 15 days ago - Pushed: 15 days ago

microbiome/mia

Microbiome analysis

* DESCRIPTION

Size: 20.8 MB - Last synced: about 13 hours ago - Pushed: about 14 hours ago

smped/ngsReports

* DESCRIPTION

Size: 38.1 MB - Last synced: 1 day ago - Pushed: 1 day ago

fmicompbio/monaLisa

binned motif enrichment analysis and visualisation

* DESCRIPTION

Size: 44.9 MB - Last synced: 5 days ago - Pushed: 5 days ago

rujinwang/EPIC

cEll tyPe enrIChment

* package/DESCRIPTION

Size: 131 MB - Last synced: 8 months ago - Pushed: over 1 year ago

gschofl/genoslideR

Handle multiple genomic alignments with annotation in R

* DESCRIPTION

Size: 2.71 MB - Last synced: about 1 year ago - Pushed: about 10 years ago

lgatto/MSnbase

Base Classes and Functions for Mass Spectrometry and Proteomics

>= 0.7.1 DESCRIPTION

Size: 96.6 MB - Last synced: 3 days ago - Pushed: 5 days ago

malemay/HaplotypeMiner

Gene-centered haplotyping from SNP data

* DESCRIPTION

Size: 471 KB - Last synced: 3 months ago - Pushed: 3 months ago

RGLab/ncdfFlow

A package that provides ncdf based storage for flow cytometry data.

* DESCRIPTION

Size: 4.84 MB - Last synced: 6 months ago - Pushed: almost 2 years ago

Simon-Coetzee/motifBreakR

A Package For Predicting The Disruptiveness Of Single Nucleotide Polymorphisms On Transcription Factor Binding Sites.

* DESCRIPTION

Size: 6.86 MB - Last synced: 11 days ago - Pushed: 11 days ago

rformassspectrometry/Spectra

Low level infrastructure to handle MS spectra

* DESCRIPTION

Size: 16.6 MB - Last synced: 5 days ago - Pushed: 6 days ago

HenrikBengtsson/aroma.affymetrix

🔬 R package: Analysis of Large Affymetrix Microarray Data Sets

>= 0.14.0 DESCRIPTION

Size: 4.05 MB - Last synced: 3 days ago - Pushed: 3 months ago

raevskymichail/epi-impute

Epi-Impute: single-cell RNA-seq imputation via integration with single-cell ATAC-seq data

* DESCRIPTION

Size: 56.3 MB - Last synced: 7 months ago - Pushed: 10 months ago

tidyomics/plyranges

A grammar of genomic data transformation

* DESCRIPTION

Size: 3.25 MB - Last synced: 10 days ago - Pushed: 24 days ago

broadinstitute/infercnv

Inferring CNV from Single-Cell RNA-Seq

* DESCRIPTION

Size: 22.6 MB - Last synced: about 1 month ago - Pushed: 2 months ago

datapplab/pathview

pathway based data integration and visualization

* DESCRIPTION

Size: 2.92 MB - Last synced: 4 days ago - Pushed: about 1 month ago

Bioconductor/BiocParallel

Bioconductor facilities for parallel evaluation

* DESCRIPTION

Size: 1.17 MB - Last synced: 4 days ago - Pushed: 4 days ago

ataudt/aneufinder

Find CNVs in single cell sequencing data.

>= 0.31.6 DESCRIPTION

Size: 35.9 MB - Last synced: 11 days ago - Pushed: about 1 year ago

cole-trapnell-lab/monocle-release

* DESCRIPTION

Size: 207 MB - Last synced: about 2 months ago - Pushed: almost 2 years ago

lgatto/MLInterfaces

Uniform interfaces to R machine learning procedures for data in Bioconductor containers - see http://bioconductor.org/packages/release/bioc/html/MLInterfaces.html for official code.

>= 0.13.11 DESCRIPTION

Size: 563 KB - Last synced: 7 months ago - Pushed: over 1 year ago

vodkatad/MatrixRider

Calculate total affinity and occupancies for binding site matrices on a given sequence

* DESCRIPTION

Size: 97.7 KB - Last synced: 9 months ago - Pushed: almost 6 years ago

GreenleafLab/ArchR

ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)

* DESCRIPTION

Size: 145 MB - Last synced: 2 months ago - Pushed: 2 months ago

bhklab/PharmacoGx

R package to analyze large-scale pharmacogenomic datasets.

* DESCRIPTION

Size: 70.8 MB - Last synced: 19 days ago - Pushed: 19 days ago

kevinblighe/PCAtools

PCAtools: everything Principal Components Analysis

* DESCRIPTION

Size: 27.5 MB - Last synced: 30 days ago - Pushed: 7 months ago

dingruofan/xQTLbiolinks

xQTLbiolinks: a comprehensive and scalable tool for integrative analysis of molecular QTLs

* DESCRIPTION

Size: 58.5 MB - Last synced: about 1 month ago - Pushed: about 1 month ago

insightsengineering/hermes

Preprocessing, analyzing, and reporting of RNA-seq data

* DESCRIPTION

Size: 45.2 MB - Last synced: 5 days ago - Pushed: 6 days ago

cytoscape/RCy3

New version of RCy3, redesigned and collaboratively maintained by Cytoscape developer community

* DESCRIPTION

Size: 19.4 MB - Last synced: 27 days ago - Pushed: about 1 month ago

MalteThodberg/CAGEfightR

Analysis of Cap Analysis of Gene Expression (CAGE) data using Bioconductor

>= 0.24.0 DESCRIPTION

Size: 13.5 MB - Last synced: 10 days ago - Pushed: over 2 years ago

shenlab-sinai/geneoverlap-old

R package for testing and visualizing gene overlaps

* DESCRIPTION

Size: 1.2 MB - Last synced: about 1 month ago - Pushed: over 7 years ago

GreenleafLab/chromVAR

chromatin Variability Across Regions (of the genome!)

* DESCRIPTION

Size: 18.8 MB - Last synced: 3 months ago - Pushed: 6 months ago

thomasp85/FindMyFriends

Fast alignment-free pangenome creation and exploration

* DESCRIPTION

Size: 1.93 MB - Last synced: 7 months ago - Pushed: about 4 years ago

DillonHammill/CytoExploreR

Interactive Cytometry Data Analysis

* DESCRIPTION

Size: 175 MB - Last synced: 13 days ago - Pushed: 13 days ago

powellgenomicslab/DropletQC

Nuclear fraction QC metric to detect empty droplets and damaged cells in scRNA-seq data

* DESCRIPTION

Size: 16.7 MB - Last synced: 11 days ago - Pushed: over 2 years ago

SunXQlab/stMLnet

stMLnet: Dissecting spatial and multilayer cell-cell communications with stMLnet

* DESCRIPTION

Size: 8.31 MB - Last synced: 10 days ago - Pushed: 11 days ago

LieberInstitute/spatialLIBD

Code for the spatialLIBD R/Bioconductor package and shiny app

* DESCRIPTION

Size: 187 MB - Last synced: 2 days ago - Pushed: 2 days ago

SofieVG/FlowSOM

Using self-organizing maps for visualization and interpretation of cytometry data

* DESCRIPTION

Size: 22 MB - Last synced: 5 months ago - Pushed: 5 months ago

griffithlab/GenVisR

Genome data visualizations

* DESCRIPTION

Size: 38 MB - Last synced: 22 days ago - Pushed: 22 days ago

BIMSBbioinfo/ciRcus

An R package for annotation of circular RNAs

* DESCRIPTION

Size: 72.3 MB - Last synced: 6 months ago - Pushed: about 4 years ago

cran/MetaIntegrator

:exclamation: This is a read-only mirror of the CRAN R package repository. MetaIntegrator — Meta-Analysis of Gene Expression Data. Homepage: http://biorxiv.org/content/early/2016/08/25/071514

* DESCRIPTION

Size: 4.69 MB - Last synced: 7 months ago - Pushed: 12 months ago

colomemaria/epiAneufinder

R package to detect breakpoints and assign somies to scATAC-seq data

* DESCRIPTION
* DESCRIPTION

Size: 31.2 MB - Last synced: 3 months ago - Pushed: 3 months ago

mfansler/txcutr

R methods for generating truncated transcript annotations

* DESCRIPTION

Size: 68.4 KB - Last synced: 17 days ago - Pushed: 17 days ago

RockefellerUniversity/profileplyr

* DESCRIPTION

Size: 9.27 MB - Last synced: about 1 year ago - Pushed: over 1 year ago

velocyto-team/velocyto.R

RNA velocity estimation in R

* DESCRIPTION

Size: 1.72 MB - Last synced: 7 months ago - Pushed: 8 months ago

tidymicrobiome/microbiomeplot

All the plot functions for tidymicrobiome

* DESCRIPTION

Size: 1.73 MB - Last synced: 9 months ago - Pushed: over 1 year ago

DarwinAwardWinner/rctutils

A collection various utility functions I have written for data analysis in R

* DESCRIPTION

Size: 320 KB - Last synced: about 1 year ago - Pushed: almost 2 years ago

kasperdanielhansen/massay

* DESCRIPTION

Size: 168 KB - Last synced: 9 months ago - Pushed: almost 9 years ago

Bioconductor/biocViews

Categorized views of R package repositories

* DESCRIPTION

Size: 1.47 MB - Last synced: 3 days ago - Pushed: 4 days ago

rformassspectrometry/QFeatures

Quantitative features for mass spectrometry data

* DESCRIPTION

Size: 20.9 MB - Last synced: 20 days ago - Pushed: 21 days ago

Rafael-Ayala/asteRisk

astrodynamics in R

* DESCRIPTION

Size: 80.9 MB - Last synced: 21 days ago - Pushed: about 2 months ago

jnpaulson/phyloseq Fork of joey711/phyloseq

phyloseq is a set of classes, wrappers, and tools (in R) to make it easier to import, store, and analyze phylogenetic sequencing data; and to reproducibly share that data and analysis with others. See the phyloseq front page:

>= 0.14.0 DESCRIPTION

Size: 70 MB - Last synced: 11 months ago - Pushed: over 8 years ago

rseng/rsepedia-analysis

Exploring clustering of research software encyclopedia entries

* _repos/github/SofieVG/FlowSOM/DESCRIPTION
* _repos/github/pmoulos/metaseqR2/DESCRIPTION

Size: 433 MB - Last synced: 3 days ago - Pushed: 5 days ago

epiviz/epivizrStandalone

Run all epiviz components locally

* DESCRIPTION

Size: 56.6 KB - Last synced: 26 days ago - Pushed: about 3 years ago

Nanostring-Biostats/GeomxTools

Tools for NanoString GeoMx Digital Spatial Profiler data for reading DCC and PKC files to NanoStringGeomxSet class, Normalization and QC.

* DESCRIPTION

Size: 82.9 MB - Last synced: 25 days ago - Pushed: 25 days ago

amcdavid/CellaRepertorium

Methods for clustering and analyzing high-throughput single cell immune cell repertoires (RepSeq)

* DESCRIPTION

Size: 16.3 MB - Last synced: 15 days ago - Pushed: almost 2 years ago

tmuetze/Bioconductor_RCy3_the_new_RCytoscape

Update RCytoscape to work for Cytoscape 3.0 and higher using CyREST

* DESCRIPTION

Size: 12.2 MB - Last synced: 6 months ago - Pushed: about 6 years ago

seandavi/GEOquery

The bridge between the NCBI Gene Expression Omnibus and Bioconductor

* DESCRIPTION

Size: 19.1 MB - Last synced: 1 day ago - Pushed: 6 months ago

kokonech/InTAD

Correlation of epigenetic signals and genes in TADs/via loops

* DESCRIPTION

Size: 517 KB - Last synced: 7 months ago - Pushed: over 2 years ago

Bioconductor/AnnotationHub

Client for the Bioconductor AnnotationHub web resource

>= 0.15.10 DESCRIPTION

Size: 1.38 MB - Last synced: 3 days ago - Pushed: 4 days ago

philliplab/MotifBinner

* DESCRIPTION

Size: 2.85 MB - Last synced: 9 months ago - Pushed: over 3 years ago

drisso/archive-EDASeq

Archived version of EDASeq

* DESCRIPTION

Size: 190 KB - Last synced: 7 months ago - Pushed: over 7 years ago

podpearson/pv

R package for analysis of Malariagen Plasmodium vivax data

* DESCRIPTION

Size: 246 KB - Last synced: about 1 year ago - Pushed: almost 11 years ago

ben-laufer/DMRichR

A R package and executable for the preprocessing, statistical analysis, and downstream testing and visualization of differentially methylated regions (DMRs) from CpG count matrices (Bismark cytosine reports)

* DESCRIPTION

Size: 4.25 MB - Last synced: 7 months ago - Pushed: 7 months ago

hjanime/Rcpi

Toolkit for Compound-Protein Interaction in Drug Discovery

* DESCRIPTION

Size: 1.79 MB - Last synced: about 1 year ago - Pushed: over 9 years ago

mjhelf/Metaboseek

Interactive software to analyze and browse mass spectrometry data

* DESCRIPTION

Size: 176 MB - Last synced: 7 months ago - Pushed: 8 months ago

Bioconductor/GenomicFeatures

Conveniently import and query gene models

>= 0.1.0 DESCRIPTION

Size: 45.7 MB - Last synced: 3 days ago - Pushed: 5 days ago

genomicsclass/ph525x

ph525x. functions only, no data

* DESCRIPTION

Size: 37.8 MB - Last synced: 9 months ago - Pushed: almost 2 years ago

MatthiasLienhard/qsea

QSEA bioconductor package

* DESCRIPTION

Size: 381 KB - Last synced: 7 months ago - Pushed: about 1 year ago

lgatto/Pbase

Manipluating and exploring protein and proteomics data

* DESCRIPTION

Size: 24.2 MB - Last synced: 7 months ago - Pushed: over 4 years ago

hbc/bcbioRNASeq

R package for bcbio RNA-seq analysis.

* DESCRIPTION

Size: 318 MB - Last synced: 15 days ago - Pushed: about 1 month ago

RGLab/flowIncubator

Routines that don't belong to the core flow packages yet.

* DESCRIPTION

Size: 199 KB - Last synced: about 1 year ago - Pushed: over 3 years ago

zhangyuqing/simulatorZ

simulates collections of independent genomic data sets, and performs within- and across-study training and validation with predicting algorithms

* DESCRIPTION

Size: 353 KB - Last synced: about 2 months ago - Pushed: over 3 years ago

lawremi/rtracklayer

R interface to genome annotation files and the UCSC genome browser

>= 0.35.3 DESCRIPTION

Size: 15.7 MB - Last synced: 2 days ago - Pushed: 2 days ago

jimhester/AllelicImbalance 📦

* DESCRIPTION

Size: 21.1 MB - Last synced: about 1 year ago - Pushed: about 9 years ago

cran/caRpools

:exclamation: This is a read-only mirror of the CRAN R package repository. caRpools — CRISPR AnalyzeR for Pooled CRISPR Screens. Homepage: http://www.crispr-analyzer.de, https://github.com/boutroslab/caRpools Report bugs for this package: https://github.com/boutroslab/caRpools

* DESCRIPTION

Size: 6.36 MB - Last synced: 7 months ago - Pushed: over 8 years ago

benjiec/xcms

* DESCRIPTION

Size: 316 KB - Last synced: 20 days ago - Pushed: over 7 years ago

zhengxwen/gdsfmt

R Interface to CoreArray Genomic Data Structure (GDS) Files (Development version only)

* DESCRIPTION

Size: 13.6 MB - Last synced: 25 days ago - Pushed: 25 days ago

songfd2018/BUSseq

R package submitted to Bioconductor

* DESCRIPTION

Size: 2.38 MB - Last synced: 17 days ago - Pushed: almost 3 years ago

andrespan/PkgedemoCDSB2022

* s4demo-main/DESCRIPTION

Size: 3.91 KB - Last synced: 9 months ago - Pushed: almost 2 years ago

tidymass/massdataset

tidymass class of dataset.

* DESCRIPTION

Size: 63.7 MB - Last synced: 4 months ago - Pushed: 4 months ago

acidgenomics/r-acidexperiment

Toolkit to extend the functionality of SummarizedExperiment.

* DESCRIPTION

Size: 835 KB - Last synced: about 2 months ago - Pushed: about 2 months ago

acidgenomics/r-pipette

Pipette biological data in and out of R.

* DESCRIPTION

Size: 3.21 MB - Last synced: about 2 months ago - Pushed: about 2 months ago

plger/scDblFinder

Methods for detecting doublets in single-cell sequencing data

* DESCRIPTION

Size: 12.3 MB - Last synced: 15 days ago - Pushed: about 2 months ago

haoharryfeng/ISLET

Individual-Specific ceLl typE referencing Tool

* DESCRIPTION

Size: 3.55 MB - Last synced: 8 months ago - Pushed: 8 months ago

adeschen/similaRpeak

Bioconductor Package - Metrics to estimate the level of similarity between two ChIP-Seq profiles

* DESCRIPTION

Size: 535 KB - Last synced: 6 months ago - Pushed: about 2 years ago

nanxstats/Rcpi

💊 Molecular informatics toolkit with integration of bioinformatics and cheminformatics tools for drug discovery

* DESCRIPTION

Size: 9.04 MB - Last synced: 10 days ago - Pushed: 10 days ago

dpryan79/BBMeth

BBMeth: An R package for fitting methylation data with a beta-binomial model

* DESCRIPTION

Size: 176 KB - Last synced: 9 months ago - Pushed: over 9 years ago

BIMIB-DISCo/TRONCO

Repository of the TRanslational ONCOlogy library, which includes various algorithms (such as CAPRESE and CAPRI) and the Pipeline for Cancer Inference (PICNIC).