Ecosyste.ms: Repos

An open API service providing repository metadata for many open source software ecosystems.

Package Usage: cran: Biobase

View more package details: https://packages.ecosyste.ms/registries/cran.r-project.org/packages/Biobase

Dependent Repos 1,262

jorainer/ensembldb
This is the ensembldb development repository.
  • * DESCRIPTION

Size: 6.57 MB - Last synced: 9 days ago - Pushed: about 1 month ago

ptelomere/RGalaxy
  • * DESCRIPTION

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

jimhester/GenomicRanges 📦
  • * DESCRIPTION

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

rscharpf/VanillaICE-release
  • * DESCRIPTION

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

pjshort/SmithLabArray
This package was developed by Tim Rayner at the CIMR (Smith Lab) but has disappeared from CRAN/Bioconductor. Adding latest stable release to my page for anyone in the group to use.
  • * DESCRIPTION
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Size: 8.54 MB - Last synced: about 1 year ago - Pushed: almost 9 years ago

gexijin/idepGolem
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Size: 5.08 MB - Last synced: 27 days ago - Pushed: 27 days ago

Sandy4321/propOverlap Fork of cran/propOverlap
Feature (gene) selection based on the Proportional Overlapping
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Size: 4.57 MB - Last synced: about 1 year ago - Pushed: over 9 years ago

Nanostring-Biostats/SpatialDecon
The SpatialDecon library implements the SpatialDecon algorithm for mixed cell deconvolution in spatial gene expression datasets. (This algorithm also works in bulk expression profiling data.)
  • * DESCRIPTION

Size: 19.6 MB - Last synced: 2 months ago - Pushed: 4 months ago

lgatto/MSnbase
Base Classes and Functions for Mass Spectrometry and Proteomics
  • >= 2.15.2 DESCRIPTION

Size: 96.9 MB - Last synced: about 23 hours ago - Pushed: 2 days ago

RGLab/ncdfFlow
A package that provides ncdf based storage for flow cytometry data.
  • * DESCRIPTION

Size: 4.84 MB - Last synced: 7 months ago - Pushed: almost 2 years ago

RGLab/luminex_R
  • * LumiR/DESCRIPTION
  • * LumiR.Rcheck/LumiR/DESCRIPTION

Size: 1.11 MB - Last synced: about 1 year ago - Pushed: about 11 years ago

zhangjunpeng411/miRSM
miRSM: Inferring miRNA sponge modules by integrating expression data and miRNA-target binding information
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Size: 3.8 MB - Last synced: 9 days ago - Pushed: about 1 month ago

chencxxy28/InteRD
Integrated and robust cell-type deconvolution
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Size: 84.3 MB - Last synced: 7 months ago - Pushed: almost 2 years ago

HenrikBengtsson/aroma.affymetrix
🔬 R package: Analysis of Large Affymetrix Microarray Data Sets
  • >= 2.28.0 DESCRIPTION

Size: 4.05 MB - Last synced: 9 days ago - Pushed: 3 months ago

raevskymichail/epi-impute
Epi-Impute: single-cell RNA-seq imputation via integration with single-cell ATAC-seq data
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Size: 56.3 MB - Last synced: 7 months ago - Pushed: 10 months ago

rickhelmus/patRoon
Workflow solutions for mass-spectrometry based non-target analysis.
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Size: 551 MB - Last synced: 12 days ago - Pushed: 12 days ago

drieslab/Giotto
Spatial omics analysis toolbox
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Size: 1.62 GB - Last synced: about 21 hours ago - Pushed: 1 day ago

stefpeschel/NetCoMi
Network construction, analysis, and comparison for microbial compositional data
  • * DESCRIPTION

Size: 16.7 MB - Last synced: 20 days ago - Pushed: 20 days ago

cole-trapnell-lab/monocle-release
  • * DESCRIPTION

Size: 207 MB - Last synced: 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.
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Size: 563 KB - Last synced: 7 months ago - Pushed: over 1 year ago

hugheylab/seeker
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Size: 31.5 MB - Last synced: 25 days ago - Pushed: 3 months ago

bhklab/PharmacoGx
R package to analyze large-scale pharmacogenomic datasets.
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Size: 70.8 MB - Last synced: about 1 month ago - Pushed: about 1 month ago

kevinblighe/PCAtools
PCAtools: everything Principal Components Analysis
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Size: 27.5 MB - Last synced: 11 days ago - Pushed: 7 months ago

insightsengineering/hermes
Preprocessing, analyzing, and reporting of RNA-seq data
  • * DESCRIPTION

Size: 45.2 MB - Last synced: 17 days ago - Pushed: 18 days ago

ErasmusMC-CCBC/katdetectr
An R package for detection, characterization and visualization of kataegis.
  • >= 2.54.0 DESCRIPTION

Size: 1.3 MB - Last synced: 3 months ago - Pushed: 3 months ago

Syksy/curatedPCaData
Curated Prostate Cancer Data R-package
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Size: 4.53 MB - Last synced: 7 months ago - Pushed: 7 months ago

thomasp85/FindMyFriends
Fast alignment-free pangenome creation and exploration
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Size: 1.93 MB - Last synced: 6 days ago - Pushed: about 4 years ago

YosefLab/ImpulseDE2
  • * DESCRIPTION

Size: 8.69 MB - Last synced: 2 months ago - Pushed: over 1 year ago

lgatto/ProteomicsAnnotationHubData
Annotation hub data for proteomics data
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Size: 106 KB - Last synced: 9 months ago - Pushed: over 2 years ago

r-forge/classpred
Read-only mirror of "classpred" from r-forge SVN.
  • * pkg/ClassPrediction/DESCRIPTION
  • * pkg/CrossValidate/DESCRIPTION
  • * pkg/GenAlgo/DESCRIPTION
  • * pkg/Modeler/DESCRIPTION

Size: 5.92 MB - Last synced: 9 months ago - Pushed: almost 2 years ago

matheuscburger/myArrayQualityMetrics
  • * DESCRIPTION

Size: 691 KB - Last synced: about 1 year ago - Pushed: about 10 years ago

currocam/HMMERutils_old 📦
A bunch of convenient functions to search for homologous sequences using the HMMER API, annotate them taxonomically, calculate physicochemical properties and facilitate exploratory analysis of homologous sequence data.
  • * DESCRIPTION

Size: 4.25 MB - Last synced: about 1 year ago - Pushed: almost 2 years ago

statOmics/tradeSeq
TRAjectory-based Differential Expression analysis for SEQuencing data
  • * DESCRIPTION

Size: 61.2 MB - Last synced: 13 days ago - Pushed: 5 months ago

dipenps/rnits
R/Bioconductor package for normalization and differential expression inference in time series gene expression microarray data
  • * DESCRIPTION

Size: 348 KB - Last synced: about 2 months ago - Pushed: about 1 year ago

mobiusklein/diffanal2
A simple differential gene expression analysis pipeline
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Size: 34 MB - Last synced: 10 months ago - Pushed: almost 10 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

hms-dbmi/dseqr
single-cell and bulk RNA-seq analyses from counts → pathways → drug candidates.
  • >= 2.46.0 DESCRIPTION

Size: 34.3 MB - Last synced: 4 days ago - Pushed: about 1 month ago

isglobal-brge/methylclock
DNA methylation-based clocks
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Size: 42 MB - Last synced: 6 days ago - Pushed: 5 months ago

tengfei/chromatoplots
  • * DESCRIPTION

Size: 1.97 MB - Last synced: about 1 month ago - Pushed: almost 11 years ago

ctlab/phantasus
Visual exploratory analysis of gene expression data
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Size: 48.7 MB - Last synced: 17 days ago - Pushed: 17 days ago

YosefLab/VISION
Signature Analysis and Visualization for Single-Cell RNA-seq
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Size: 94.6 MB - Last synced: 4 days ago - Pushed: 3 months ago

ShixiangWang/sigminer
🌲 An easy-to-use and scalable toolkit for genomic alteration signature (a.k.a. mutational signature) analysis and visualization in R https://shixiangwang.github.io/sigminer/reference/index.html
  • * DESCRIPTION

Size: 51 MB - Last synced: about 1 month ago - Pushed: 2 months 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
  • >= 2.21.5 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: 9 days ago - Pushed: 16 days ago

rformassspectrometry/QFeatures
Quantitative features for mass spectrometry data
  • * DESCRIPTION

Size: 21.4 MB - Last synced: 3 days ago - Pushed: 4 days ago

msettles/rSFFreader
R packages for flow gram based sequence data Roche 454 and Ion Torrent
  • * DESCRIPTION

Size: 4.35 MB - Last synced: 2 months ago - Pushed: almost 11 years ago

netZoo/netZooR
netZooR is a network biology package implemented in R.
  • * DESCRIPTION

Size: 530 MB - Last synced: 2 months ago - Pushed: 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:
  • >= 2.0.0 DESCRIPTION

Size: 70 MB - Last synced: 12 months ago - Pushed: over 8 years ago

xuranw/MuSiC
Multi-subject Single Cell Deconvolution
  • * DESCRIPTION

Size: 133 MB - Last synced: 2 months ago - Pushed: 2 months ago

RGLab/ImmuneSpaceR
An R Interface to the ImmuneSpace database portal
  • * DESCRIPTION

Size: 81.3 MB - Last synced: 27 days ago - Pushed: 6 months ago

rseng/rsepedia-analysis
Exploring clustering of research software encyclopedia entries
  • * _repos/github/ShixiangWang/sigminer/DESCRIPTION
  • * _repos/github/metaOmics/MetaPath/DESCRIPTION
  • * _repos/github/pmoulos/metaseqR2/DESCRIPTION
  • * _repos/github/rickhelmus/patRoon/DESCRIPTION
  • * _repos/github/ropensci/BaseSet/DESCRIPTION

Size: 435 MB - Last synced: 2 days ago - Pushed: 3 days ago

MassDynamics/lfq_processing
Post-processing of MaxQuant Label Free Quantification results.
  • * DESCRIPTION

Size: 51.9 MB - Last synced: 7 months ago - Pushed: about 1 year ago

epiviz/epivizrStandalone
Run all epiviz components locally
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Size: 56.6 KB - Last synced: about 1 month 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: about 1 month ago - Pushed: about 1 month ago

camilleroquencourt/ptairMS
  • * DESCRIPTION

Size: 17.2 MB - Last synced: 14 days ago - Pushed: 24 days ago

seandavi/GEOquery
The bridge between the NCBI Gene Expression Omnibus and Bioconductor
  • * DESCRIPTION

Size: 19.1 MB - Last synced: 2 days 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

lia978/ggheatmap
code for ggheatmap package
  • * DESCRIPTION

Size: 24.5 MB - Last synced: about 1 year ago - Pushed: over 8 years ago

drisso/archive-EDASeq
Archived version of EDASeq
  • >= 2.15.1 DESCRIPTION

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

RTCGA/RTCGA
Download, integration and visualizations of the variety & volume of TCGA data.
  • * DESCRIPTION

Size: 17.8 MB - Last synced: 8 days ago - Pushed: over 1 year ago

facilebio/FacileData
A fluent, tidy-like API for accessing multi-assay high-throughput genomics data
  • * DESCRIPTION

Size: 34.8 MB - Last synced: 17 days ago - Pushed: 3 months ago

PeteHaitch/methsim
An R package to simulate DNA methylation data.
  • * DESCRIPTION

Size: 16.3 MB - Last synced: about 1 year ago - Pushed: almost 8 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: 8 months ago - Pushed: 8 months ago

Distue/limmas
Linear models for mass spectrometry
  • * limmas/DESCRIPTION

Size: 4.88 MB - Last synced: 7 months ago - Pushed: over 8 years ago

mjhelf/Metaboseek
Interactive software to analyze and browse mass spectrometry data
  • * DESCRIPTION

Size: 176 MB - Last synced: 7 months ago - Pushed: 9 months ago

Bioconductor/GenomicFeatures
Conveniently import and query gene models
  • >= 2.15.1 DESCRIPTION

Size: 45.7 MB - Last synced: 9 days ago - Pushed: 17 days ago

genomicsclass/ph525x
ph525x. functions only, no data
  • * DESCRIPTION
  • * DESCRIPTION

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

pimentel/DESeq2paper
A fork of http://www-huber.embl.de/DESeq2paper/
  • * DESCRIPTION

Size: 2.7 MB - Last synced: 7 months ago - Pushed: almost 9 years ago

eahrne/SafeQuant
A Toolbox for analysis of Proteomics Data
  • * DESCRIPTION

Size: 498 MB - Last synced: 7 months ago - Pushed: about 3 years ago

omnideconv/immunedeconv
A unified interface to immune deconvolution methods (CIBERSORT, EPIC, quanTIseq, TIMER, xCell, MCPcounter) and mouse deconvolution methods
  • * DESCRIPTION

Size: 118 MB - Last synced: 4 days ago - Pushed: 11 days ago

adamsardar/metaDEGth
metaDEGth: meta-analysis of Differentially Expressed Genes using parametric, empirically-derived P-value distributions
  • >= 2.4 DESCRIPTION

Size: 15.8 MB - Last synced: 7 months ago - Pushed: over 1 year ago

isglobal-brge/dsExposome
DataSHIELD server functions for the exposome data analysis
  • * DESCRIPTION

Size: 211 KB - Last synced: about 1 year ago - Pushed: over 1 year ago

RGLab/HIV.db
HIV annotation database
  • >= 2.5.5 DESCRIPTION

Size: 1.36 MB - Last synced: about 1 year ago - Pushed: over 8 years ago

ImmuneDynamics/Spectre
A computational toolkit in R for the integration, exploration, and analysis of high-dimensional single-cell cytometry and imaging data.
  • * DESCRIPTION

Size: 602 MB - Last synced: 6 days ago - Pushed: 23 days ago

lgatto/Pbase
Manipluating and exploring protein and proteomics data
  • * DESCRIPTION

Size: 24.2 MB - Last synced: 7 months ago - Pushed: almost 5 years ago

bnikolic/rpkg-hexbin
R Package hexbin
  • * DESCRIPTION

Size: 656 KB - Last synced: 7 months ago - Pushed: almost 12 years ago

ctlab/GAM 📦
Integrated analysis of transcriptional and metabolic profiling
  • * mouseMacrophages/DESCRIPTION

Size: 1.05 MB - Last synced: about 1 month ago - Pushed: almost 2 years ago

sneumann/MetShot
R package for Nearline acquisition and processing of tandem-MS data
  • * DESCRIPTION

Size: 6.93 MB - Last synced: 7 months ago - Pushed: almost 6 years ago

kohak/CMDA
CMDA Class
  • * hexbin_1.27.0/hexbin/DESCRIPTION

Size: 2.85 MB - Last synced: 25 days ago - Pushed: over 9 years ago

GeorgeAlehandro/cipheinfinityFlow
Fork done to modify some functionalities of the original package
  • * DESCRIPTION

Size: 4.17 MB - Last synced: about 1 year ago - Pushed: almost 2 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: 2 months ago - Pushed: over 3 years ago

benjiec/xcms
  • * DESCRIPTION

Size: 316 KB - Last synced: about 1 month ago - Pushed: over 7 years ago

MassDynamics/MassExpression
Universal Imports + High Quality QC + Differential Expression Analysis = Awesomeness.
  • >= 2.46.0 DESCRIPTION

Size: 21.8 MB - Last synced: about 1 year ago - Pushed: about 1 year ago

cran/vbmp
Variational Bayesian Multinomial Probit Regression
  • >= 2.5.5 DESCRIPTION

Size: 4 MB - Last synced: 9 months ago - Pushed: about 10 years ago

rikenbit/PubMedQuery
PubMedQuery is an R package for retrieve PubMed documents
  • * OtherPackages/GEOquery/DESCRIPTION

Size: 26.5 MB - Last synced: 6 months ago - Pushed: almost 10 years ago

acidgenomics/r-acidexperiment
Toolkit to extend the functionality of SummarizedExperiment.
  • * DESCRIPTION

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

renzhonglu/ConsensusClusterPlus
This is a read-only mirror of the Bioconductor SVN repository. Package Homepage: http://bioconductor.org/packages/devel/bioc/html/ConsensusClusterPlus.html Bug Reports: https://support.bioconductor.org/p/new/post/?tag_val=ConsensusClusterPlus.
  • * DESCRIPTION

Size: 164 KB - Last synced: 7 months ago - Pushed: almost 9 years ago

vsbuffalo/tasselr
Some beta interfaces to Tassel's GBS data on HDF5
  • * DESCRIPTION

Size: 305 KB - Last synced: about 1 month ago - Pushed: about 9 years ago

cran/Statomica
:exclamation: This is a read-only mirror of the CRAN R package repository. Statomica — Statomica utility package. Homepage: http://www.cran.r-project.org, http://www.bioconductor.org, http://www.statomics.com
  • * DESCRIPTION

Size: 301 KB - Last synced: 9 months ago - Pushed: over 9 years ago