Ecosyste.ms: Packages

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bioconductor.org packages

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hypeR 2.2.0
An R Package For Geneset Enrichment Workflows
3 versions - Latest release: 37 minutes ago - 8.49 thousand downloads total - 65 stars on GitHub - 1 maintainer
Top 5.0% on bioconductor.org
CGHbase 1.64.0
CGHbase: Base functions and classes for arrayCGH data analysis.
3 versions - Latest release: about 2 hours ago - 6 dependent packages - 71.8 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 2.7% on bioconductor.org
TCGAbiolinks 2.32.0
TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data
4 versions - Latest release: about 2 hours ago - 6 dependent packages - 364 thousand downloads total - 274 stars on GitHub - 2 maintainers
Top 2.7% on bioconductor.org
gdsfmt 1.40.0
R Interface to CoreArray Genomic Data Structure (GDS) Files
3 versions - Latest release: about 2 hours ago - 18 dependent packages - 211 thousand downloads total - 18 stars on GitHub - 1 maintainer
SpotClean 1.6.0
SpotClean adjusts for spot swapping in spatial transcriptomics data
4 versions - Latest release: about 2 hours ago - 2.83 thousand downloads total - 13 stars on GitHub - 1 maintainer
Top 5.8% on bioconductor.org
ssize 1.78.0
Estimate Microarray Sample Size
3 versions - Latest release: about 3 hours ago - 40.4 thousand downloads total - 1 maintainer
GeoDiff 1.10.0
Count model based differential expression and normalization on GeoMx RNA data
3 versions - Latest release: about 3 hours ago - 3.75 thousand downloads total - 7 stars on GitHub - 1 maintainer
Top 4.2% on bioconductor.org
piano 2.20.0
Platform for integrative analysis of omics data
3 versions - Latest release: about 3 hours ago - 3 dependent packages - 68.9 thousand downloads total - 1 maintainer
Top 4.3% on bioconductor.org
plyranges 1.24.0
A fluent interface for manipulating GenomicRanges
3 versions - Latest release: about 4 hours ago - 19 dependent packages - 74.9 thousand downloads total - 127 stars on GitHub - 1 maintainer
Top 4.8% on bioconductor.org
NormqPCR 1.50.0
Functions for normalisation of RT-qPCR data
3 versions - Latest release: about 5 hours ago - 56.9 thousand downloads total - 1 maintainer
Top 5.3% on bioconductor.org
CGHcall 2.66.0
Calling aberrations for array CGH tumor profiles.
3 versions - Latest release: about 5 hours ago - 3 dependent packages - 66.2 thousand downloads total - 1 maintainer
Top 5.7% on bioconductor.org
flowAI 1.34.0
Automatic and interactive quality control for flow cytometry data
3 versions - Latest release: about 6 hours ago - 1 dependent package - 52.1 thousand downloads total - 1 maintainer
CytoPipeline 1.4.0
Automation and visualization of flow cytometry data analysis pipelines
3 versions - Latest release: about 6 hours ago - 1 dependent package - 1.79 thousand downloads total - 3 stars on GitHub - 1 maintainer
netresponse 1.64.0
Functional Network Analysis
3 versions - Latest release: about 6 hours ago - 25.1 thousand downloads total - 3 stars on GitHub - 1 maintainer
scatterHatch 1.10.0
Creates hatched patterns for scatterplots
3 versions - Latest release: about 6 hours ago - 1.96 thousand downloads total - 5 stars on GitHub - 1 maintainer
Top 2.2% on bioconductor.org
flowViz 1.68.0
Visualization for flow cytometry
3 versions - Latest release: about 6 hours ago - 11 dependent packages - 280 thousand downloads total - 1 maintainer
Top 5.9% on bioconductor.org
EBarrays 2.68.0
Unified Approach for Simultaneous Gene Clustering and Differential Expression Identification
3 versions - Latest release: about 6 hours ago - 6 dependent packages - 55.6 thousand downloads total - 1 maintainer
CDI 1.2.0
Clustering Deviation Index (CDI)
3 versions - Latest release: about 7 hours ago - 778 downloads total - 7 stars on GitHub - 1 maintainer
ptairMS 1.12.0
Pre-processing PTR-TOF-MS Data
3 versions - Latest release: about 7 hours ago - 2.85 thousand downloads total - 7 stars on GitHub - 1 maintainer
gDNAx 1.2.0
Diagnostics for assessing genomic DNA contamination in RNA-seq data
4 versions - Latest release: about 7 hours ago - 1.06 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 4.5% on bioconductor.org
ArrayExpress 1.64.0
Access the ArrayExpress Collection at EMBL-EBI Biostudies and build Bioconductor data structures:...
3 versions - Latest release: about 8 hours ago - 1 dependent package - 131 thousand downloads total - 1 maintainer
Top 2.1% on bioconductor.org
mzID 1.42.0
An mzIdentML parser for R
3 versions - Latest release: about 8 hours ago - 5 dependent packages - 265 thousand downloads total - 1 maintainer
Top 3.2% on bioconductor.org
lpsymphony 1.32.0
Symphony integer linear programming solver in R
3 versions - Latest release: about 9 hours ago - 1 dependent package - 128 thousand downloads total - 1 maintainer
Top 3.6% on bioconductor.org
Icens 1.76.0
NPMLE for Censored and Truncated Data
3 versions - Latest release: about 9 hours ago - 1 dependent package - 123 thousand downloads total - 1 maintainer
Top 3.8% on bioconductor.org
aroma.light 3.34.0
Light-Weight Methods for Normalization and Visualization of Microarray Data using Only Basic R Da...
3 versions - Latest release: about 9 hours ago - 3 dependent packages - 324 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 2.9% on bioconductor.org
metapod 1.12.0
Meta-Analyses on P-Values of Differential Analyses
4 versions - Latest release: about 10 hours ago - 4 dependent packages - 204 thousand downloads total - 1 maintainer
Top 4.7% on bioconductor.org
RnBeads 2.22.0
RnBeads
3 versions - Latest release: about 10 hours ago - 1 dependent package - 54.4 thousand downloads total - 1 maintainer
Top 3.5% on bioconductor.org
Heatplus 3.12.0
Heatmaps with row and/or column covariates and colored clusters
3 versions - Latest release: about 10 hours ago - 2 dependent packages - 133 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 4.4% on bioconductor.org
tkWidgets 1.82.0
R based tk widgets
3 versions - Latest release: about 11 hours ago - 7 dependent packages - 198 thousand downloads total - 1 maintainer
Top 4.4% on bioconductor.org
SC3 1.32.0
Single-Cell Consensus Clustering
3 versions - Latest release: about 11 hours ago - 4 dependent packages - 63.4 thousand downloads total - 115 stars on GitHub - 1 maintainer
Top 4.5% on bioconductor.org
GENIE3 1.26.0
GEne Network Inference with Ensemble of trees
3 versions - Latest release: about 11 hours ago - 2 dependent packages - 73 thousand downloads total - 1 maintainer
Top 3.3% on bioconductor.org
DMRcate 3.0.0
Methylation array and sequencing spatial analysis methods
4 versions - Latest release: about 11 hours ago - 2 dependent packages - 135 thousand downloads total - 1 maintainer
Top 4.5% on bioconductor.org
genefu 2.36.0
Computation of Gene Expression-Based Signatures in Breast Cancer
3 versions - Latest release: about 12 hours ago - 3 dependent packages - 66.7 thousand downloads total - 1 maintainer
scBubbletree 1.6.0
Quantitative visual exploration of scRNA-seq data
3 versions - Latest release: about 12 hours ago - 1.59 thousand downloads total - 4 stars on GitHub - 1 maintainer
Top 3.6% on bioconductor.org
motifStack 1.48.0
Plot stacked logos for single or multiple DNA, RNA and amino acid sequence
3 versions - Latest release: about 12 hours ago - 10 dependent packages - 106 thousand downloads total - 1 maintainer
ScaledMatrix 1.12.0
Creating a DelayedMatrix of Scaled and Centered Values
3 versions - Latest release: about 12 hours ago - 5 dependent packages - 505 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 2.8% on bioconductor.org
RUVSeq 1.38.0
Remove Unwanted Variation from RNA-Seq Data
3 versions - Latest release: about 14 hours ago - 7 dependent packages - 141 thousand downloads total - 13 stars on GitHub - 1 maintainer
Top 4.1% on bioconductor.org
motifmatchr 1.26.0
Fast Motif Matching in R
3 versions - Latest release: about 14 hours ago - 10 dependent packages - 90.2 thousand downloads total - 1 maintainer
Top 2.9% on bioconductor.org
flowStats 4.16.0
Statistical methods for the analysis of flow cytometry data
4 versions - Latest release: about 14 hours ago - 9 dependent packages - 183 thousand downloads total - 15 stars on GitHub - 2 maintainers
scFeatures 1.4.0
scFeatures: Multi-view representations of single-cell and spatial data for disease outcome predic...
4 versions - Latest release: about 14 hours ago - 1.45 thousand downloads total - 10 stars on GitHub - 1 maintainer
Top 5.1% on bioconductor.org
pdInfoBuilder 1.68.0
Platform Design Information Package Builder
3 versions - Latest release: about 14 hours ago - 49.9 thousand downloads total - 1 maintainer
Top 4.5% on bioconductor.org
AUCell 1.26.0
AUCell: Analysis of 'gene set' activity in single-cell RNA-seq data (e.g. identify cells with spe...
3 versions - Latest release: about 14 hours ago - 3 dependent packages - 126 thousand downloads total - 1 maintainer
SVMDO 1.4.0
Identification of Tumor-Discriminating mRNA Signatures via Support Vector Machines Supported by D...
5 versions - Latest release: about 14 hours ago - 1.91 thousand downloads total - 0 stars on GitHub - 1 maintainer
PureCN 2.10.0
Copy number calling and SNV classification using targeted short read sequencing
4 versions - Latest release: about 15 hours ago - 25.8 thousand downloads total - 120 stars on GitHub - 1 maintainer
Top 4.6% on bioconductor.org
frma 1.56.0
Frozen RMA and Barcode
3 versions - Latest release: about 15 hours ago - 2 dependent packages - 62.5 thousand downloads total - 1 maintainer
Top 3.6% on bioconductor.org
NOISeq 2.48.0
Exploratory analysis and differential expression for RNA-seq data
3 versions - Latest release: about 16 hours ago - 5 dependent packages - 101 thousand downloads total - 1 maintainer
Top 5.4% on bioconductor.org
limmaGUI 1.80.0
GUI for limma Package With Two Color Microarrays
3 versions - Latest release: about 16 hours ago - 48.9 thousand downloads total - 1 maintainer
Top 5.3% on bioconductor.org
puma 3.46.0
Propagating Uncertainty in Microarray Analysis(including Affymetrix tranditional 3' arrays and ex...
3 versions - Latest release: about 16 hours ago - 1 dependent package - 46.1 thousand downloads total - 1 maintainer
Top 5.6% on bioconductor.org
HTqPCR 1.58.0
Automated analysis of high-throughput qPCR data
3 versions - Latest release: about 16 hours ago - 2 dependent packages - 52.6 thousand downloads total - 1 maintainer
Top 3.0% on bioconductor.org
batchelor 1.20.0
Single-Cell Batch Correction Methods
4 versions - Latest release: about 16 hours ago - 5 dependent packages - 244 thousand downloads total - 1 maintainer
Top 5.3% on bioconductor.org
bioDist 1.76.0
Different distance measures
3 versions - Latest release: about 16 hours ago - 2 dependent packages - 88.6 thousand downloads total - 1 maintainer
Top 4.4% on bioconductor.org
PROcess 1.80.0
Ciphergen SELDI-TOF Processing
3 versions - Latest release: about 17 hours ago - 59.6 thousand downloads total - 1 maintainer
Top 3.8% on bioconductor.org
fastseg 1.50.0
fastseg - a fast segmentation algorithm
3 versions - Latest release: about 17 hours ago - 1 dependent package - 94.3 thousand downloads total - 1 maintainer
OutSplice 1.4.0
Comparison of Splicing Events between Tumor and Normal Samples
3 versions - Latest release: about 17 hours ago - 1.13 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 5.1% on bioconductor.org
M3C 1.26.0
Monte Carlo Reference-based Consensus Clustering
3 versions - Latest release: about 18 hours ago - 63.2 thousand downloads total - 1 maintainer
Top 4.0% on bioconductor.org
apeglm 1.26.0
Approximate posterior estimation for GLM coefficients
3 versions - Latest release: about 18 hours ago - 10 dependent packages - 252 thousand downloads total - 1 maintainer
Top 5.0% on bioconductor.org
seqPattern 1.36.0
Visualising oligonucleotide patterns and motif occurrences across a set of sorted sequences
3 versions - Latest release: about 18 hours ago - 2 dependent packages - 55.6 thousand downloads total - 1 maintainer
Top 4.3% on bioconductor.org
GEOmetadb 1.66.0
A compilation of metadata from NCBI GEO
3 versions - Latest release: about 19 hours ago - 74.9 thousand downloads total - 1 maintainer
Top 3.3% on bioconductor.org
minet 3.62.0
Mutual Information NETworks
3 versions - Latest release: about 19 hours ago - 9 dependent packages - 122 thousand downloads total - 1 maintainer
Top 2.7% on bioconductor.org
affycoretools 1.76.0
Functions useful for those doing repetitive analyses with Affymetrix GeneChips
3 versions - Latest release: about 19 hours ago - 2 dependent packages - 119 thousand downloads total - 1 maintainer
Top 5.7% on bioconductor.org
OrderedList 1.76.0
Similarities of Ordered Gene Lists
3 versions - Latest release: about 19 hours ago - 43.5 thousand downloads total - 1 maintainer
Top 5.9% on bioconductor.org
survcomp 1.54.0
Performance Assessment and Comparison for Survival Analysis
3 versions - Latest release: about 20 hours ago - 4 dependent packages - 125 thousand downloads total - 1 maintainer
Top 4.1% on bioconductor.org
makecdfenv 1.80.0
CDF Environment Maker
3 versions - Latest release: about 20 hours ago - 1 dependent package - 75.9 thousand downloads total - 1 maintainer
Top 2.0% on bioconductor.org
monocle 2.32.0
Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq
4 versions - Latest release: about 20 hours ago - 6 dependent packages - 313 thousand downloads total - 1 maintainer
simpleSeg 1.6.0
A package to perform simple cell segmentation
4 versions - Latest release: about 20 hours ago - 1.85 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 3.7% on bioconductor.org
InteractionSet 1.32.0
Base Classes for Storing Genomic Interaction Data
3 versions - Latest release: about 20 hours ago - 20 dependent packages - 109 thousand downloads total - 1 maintainer
Top 2.2% on bioconductor.org
EDASeq 2.38.0
Exploratory Data Analysis and Normalization for RNA-Seq
3 versions - Latest release: about 21 hours ago - 12 dependent packages - 313 thousand downloads total - 4 stars on GitHub - 1 maintainer
Top 5.3% on bioconductor.org
RedeR 3.0.0
Interactive visualization and manipulation of nested networks
4 versions - Latest release: about 21 hours ago - 4 dependent packages - 48.3 thousand downloads total - 1 maintainer
Top 5.0% on bioconductor.org
microRNA 1.62.0
Data and functions for dealing with microRNAs
3 versions - Latest release: about 21 hours ago - 1 dependent package - 61.6 thousand downloads total - 1 maintainer
Top 4.8% on bioconductor.org
CAMERA 1.60.0
Collection of annotation related methods for mass spectrometry data
3 versions - Latest release: about 21 hours ago - 8 dependent packages - 108 thousand downloads total - 1 maintainer
fgga 1.12.0
Hierarchical ensemble method based on factor graph
4 versions - Latest release: about 22 hours ago - 3.07 thousand downloads total - 3 stars on GitHub - 1 maintainer
Top 3.4% on bioconductor.org
QuasR 1.44.0
Quantify and Annotate Short Reads in R
3 versions - Latest release: about 22 hours ago - 2 dependent packages - 92.3 thousand downloads total - 1 maintainer
Top 3.2% on bioconductor.org
DSS 2.52.0
Dispersion shrinkage for sequencing data
4 versions - Latest release: about 22 hours ago - 10 dependent packages - 146 thousand downloads total - 2 maintainers
Top 4.9% on bioconductor.org
scde 2.32.0
Single Cell Differential Expression
3 versions - Latest release: about 22 hours ago - 54.1 thousand downloads total - 1 maintainer
Top 3.2% on bioconductor.org
DropletUtils 1.24.0
Utilities for Handling Single-Cell Droplet Data
3 versions - Latest release: about 22 hours ago - 12 dependent packages - 171 thousand downloads total - 1 maintainer
Top 4.3% on bioconductor.org
slingshot 2.12.0
Tools for ordering single-cell sequencing
3 versions - Latest release: about 22 hours ago - 4 dependent packages - 89.5 thousand downloads total - 225 stars on GitHub - 1 maintainer
Top 3.3% on bioconductor.org
quantsmooth 1.70.0
Quantile smoothing and genomic visualization of array data
3 versions - Latest release: about 22 hours ago - 4 dependent packages - 99.4 thousand downloads total - 1 maintainer
Top 2.3% on bioconductor.org
ncdfFlow 2.50.0
ncdfFlow: A package that provides HDF5 based storage for flow cytometry data.
3 versions - Latest release: about 22 hours ago - 6 dependent packages - 218 thousand downloads total - 1 maintainer
Top 3.2% on bioconductor.org
oligo 1.68.0
Preprocessing tools for oligonucleotide arrays
3 versions - Latest release: about 22 hours ago - 11 dependent packages - 368 thousand downloads total - 1 maintainer
Top 4.8% on bioconductor.org
affylmGUI 1.78.0
GUI for limma Package with Affymetrix Microarrays
3 versions - Latest release: about 22 hours ago - 66 thousand downloads total - 1 maintainer
Top 2.8% on bioconductor.org
msa 1.36.0
Multiple Sequence Alignment
3 versions - Latest release: about 22 hours ago - 4 dependent packages - 175 thousand downloads total - 14 stars on GitHub - 1 maintainer
Top 5.7% on bioconductor.org
GenVisR 1.36.0
Genomic Visualizations in R
3 versions - Latest release: about 22 hours ago - 50.3 thousand downloads total - 194 stars on GitHub - 1 maintainer
Top 4.2% on bioconductor.org
bluster 1.14.0
Clustering Algorithms for Bioconductor
3 versions - Latest release: about 22 hours ago - 11 dependent packages - 236 thousand downloads total - 1 maintainer
Top 4.1% on bioconductor.org
Rdisop 1.64.0
Decomposition of Isotopic Patterns
3 versions - Latest release: about 22 hours ago - 2 dependent packages - 72.7 thousand downloads total - 4 stars on GitHub - 1 maintainer
extraChIPs 1.8.1
Additional functions for working with ChIP-Seq data
5 versions - Latest release: about 23 hours ago - 2.42 thousand downloads total - 7 stars on GitHub - 1 maintainer
Top 4.3% on bioconductor.org
ChAMP 2.34.0
Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC
3 versions - Latest release: about 23 hours ago - 1 dependent package - 117 thousand downloads total - 1 maintainer
Top 4.4% on bioconductor.org
csaw 1.38.0
ChIP-Seq Analysis with Windows
4 versions - Latest release: about 23 hours ago - 8 dependent packages - 72.1 thousand downloads total - 1 maintainer
BiocFHIR 1.6.0
Illustration of FHIR ingestion and transformation using R
3 versions - Latest release: about 23 hours ago - 1.55 thousand downloads total - 3 stars on GitHub - 1 maintainer
Top 2.5% on bioconductor.org
MultiAssayExperiment 1.30.1
Software for the integration of multi-omics experiments in Bioconductor
3 versions - Latest release: about 23 hours ago - 57 dependent packages - 245 thousand downloads total - 1 maintainer
timeOmics 1.16.0
Time-Course Multi-Omics data integration
3 versions - Latest release: about 23 hours ago - 1 dependent package - 5.04 thousand downloads total - 21 stars on GitHub - 1 maintainer
Top 5.9% on bioconductor.org
OCplus 1.78.0
Operating characteristics plus sample size and local fdr for microarray experiments
3 versions - Latest release: about 23 hours ago - 41.6 thousand downloads total - 1 maintainer
Top 3.8% on bioconductor.org
baySeq 2.38.0
Empirical Bayesian analysis of patterns of differential expression in count data
3 versions - Latest release: about 23 hours ago - 6 dependent packages - 122 thousand downloads total - 1 maintainer
Top 5.5% on bioconductor.org
dupRadar 1.34.0
Assessment of duplication rates in RNA-Seq datasets
3 versions - Latest release: about 23 hours ago - 51.4 thousand downloads total - 1 stars on GitHub - 2 maintainers
Top 4.3% on bioconductor.org
basilisk 1.16.0
Freezing Python Dependencies Inside Bioconductor Packages
5 versions - Latest release: about 24 hours ago - 26 dependent packages - 143 thousand downloads total - 24 stars on GitHub - 1 maintainer
Top 4.6% on bioconductor.org
sangerseqR 1.40.0
Tools for Sanger Sequencing Data in R
3 versions - Latest release: about 24 hours ago - 3 dependent packages - 63.7 thousand downloads total - 1 maintainer
benchdamic 1.10.0
Benchmark of differential abundance methods on microbiome data
5 versions - Latest release: about 24 hours ago - 3.07 thousand downloads total - 5 stars on GitHub - 1 maintainer
Top 4.6% on bioconductor.org
chipseq 1.54.0
chipseq: A package for analyzing chipseq data
3 versions - Latest release: 1 day ago - 4 dependent packages - 115 thousand downloads total - 1 maintainer
Top 4.3% on bioconductor.org
crlmm 1.62.0
Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumin...
3 versions - Latest release: 1 day ago - 3 dependent packages - 69.9 thousand downloads total - 3 maintainers
Top 5.0% on bioconductor.org
HMMcopy 1.46.0
Copy number prediction with correction for GC and mappability bias for HTS data
3 versions - Latest release: 1 day ago - 1 dependent package - 64.3 thousand downloads total - 1 maintainer
Top 5.6% on bioconductor.org
PICS 2.48.0
Probabilistic inference of ChIP-seq
3 versions - Latest release: 1 day ago - 1 dependent package - 42.8 thousand downloads total - 0 stars on GitHub - 1 maintainer