bioconductor.org "bioinformatics" keyword
View the packages on the bioconductor.org package registry that are tagged with the "bioinformatics" keyword.
simPIC 1.4.0
simPIC: flexible simulation of paired-insertion counts for single-cell ATAC-sequencing data3 versions - Latest release: 5 months ago - 3.65 thousand downloads total - 0 stars on GitHub - 1 maintainer
rWikiPathways 1.28.0
rWikiPathways - R client library for the WikiPathways API5 versions - Latest release: 5 months ago - 5 dependent packages - 70.1 thousand downloads total - 17 stars on GitHub - 1 maintainer
Top 1.5% on bioconductor.org
5 versions - Latest release: 5 months ago - 9 dependent packages - 287 thousand downloads total - 472 stars on GitHub - 1 maintainer
maftools 2.24.0 💰
Summarize, Analyze and Visualize MAF Files5 versions - Latest release: 5 months ago - 9 dependent packages - 287 thousand downloads total - 472 stars on GitHub - 1 maintainer
Top 1.9% on bioconductor.org
7 versions - Latest release: 4 months ago - 30 dependent packages - 495 thousand downloads total - 123 stars on GitHub - 1 maintainer
MSnbase 2.34.1
Base Functions and Classes for Mass Spectrometry and Proteomics7 versions - Latest release: 4 months ago - 30 dependent packages - 495 thousand downloads total - 123 stars on GitHub - 1 maintainer
Top 1.4% on bioconductor.org
5 versions - Latest release: 5 months ago - 47 dependent packages - 2.14 million downloads total - 98 stars on GitHub - 1 maintainer
GEOquery 2.76.0
Get data from NCBI Gene Expression Omnibus (GEO)5 versions - Latest release: 5 months ago - 47 dependent packages - 2.14 million downloads total - 98 stars on GitHub - 1 maintainer
Top 5.6% on bioconductor.org
7 versions - Latest release: 5 months ago - 4 dependent packages - 73.1 thousand downloads total - 78 stars on GitHub - 1 maintainer
sesame 1.26.0
SEnsible Step-wise Analysis of DNA MEthylation BeadChips7 versions - Latest release: 5 months ago - 4 dependent packages - 73.1 thousand downloads total - 78 stars on GitHub - 1 maintainer
Top 2.7% on bioconductor.org
5 versions - Latest release: 4 months ago - 11 dependent packages - 310 thousand downloads total - 8 stars on GitHub - 1 maintainer
graphite 1.54.0
GRAPH Interaction from pathway Topological Environment5 versions - Latest release: 4 months ago - 11 dependent packages - 310 thousand downloads total - 8 stars on GitHub - 1 maintainer
POMA 1.18.0
Tools for Omics Data Analysis5 versions - Latest release: 4 months ago - 1 dependent package - 11.6 thousand downloads total - 12 stars on GitHub - 1 maintainer
BioCor 1.32.0
Functional similarities5 versions - Latest release: 4 months ago - 19 thousand downloads total - 14 stars on GitHub - 1 maintainer
pathlinkR 1.4.0
Analyze and interpret RNA-Seq results4 versions - Latest release: 4 months ago - 4.63 thousand downloads total - 29 stars on GitHub - 1 maintainer
gemma.R 3.4.5
A wrapper for Gemma's Restful API to access curated gene expression data and differential express...16 versions - Latest release: about 2 months ago - 6.94 thousand downloads total - 10 stars on GitHub - 1 maintainer
ontoProc 2.2.1
processing of ontologies of anatomy, cell lines, and so on7 versions - Latest release: 3 months ago - 3 dependent packages - 21.4 thousand downloads total - 5 stars on GitHub - 1 maintainer
MungeSumstats 1.16.0
Standardise summary statistics from GWAS7 versions - Latest release: 4 months ago - 43.3 thousand downloads total - 85 stars on GitHub - 1 maintainer
doubletrouble 1.8.1
Identification and classification of duplicated genes12 versions - Latest release: about 1 month ago - 6.3 thousand downloads total - 27 stars on GitHub - 1 maintainer
rmelting 1.24.0
R Interface to MELTING 55 versions - Latest release: 5 months ago - 10.8 thousand downloads total - 2 stars on GitHub - 1 maintainer
getDEE2 1.18.0
Programmatic access to the DEE2 RNA expression dataset6 versions - Latest release: 4 months ago - 8.22 thousand downloads total - 4 stars on GitHub - 1 maintainer
SGCP 1.8.0
SGCP: A semi-supervised pipeline for gene clustering using self-training approach in gene co-expr...7 versions - Latest release: 5 months ago - 5.87 thousand downloads total - 2 stars on GitHub - 1 maintainer
sparrow 1.14.0
Take command of set enrichment analyses through a unified interface6 versions - Latest release: 5 months ago - 1 dependent package - 14.1 thousand downloads total - 22 stars on GitHub - 1 maintainer
Top 3.2% on bioconductor.org
7 versions - Latest release: 4 months ago - 11 dependent packages - 218 thousand downloads total - 108 stars on GitHub - 1 maintainer
SNPRelate 1.42.0
Parallel Computing Toolset for Relatedness and Principal Component Analysis of SNP Data7 versions - Latest release: 4 months ago - 11 dependent packages - 218 thousand downloads total - 108 stars on GitHub - 1 maintainer
hypeR 2.5.0
An R Package For Geneset Enrichment Workflows5 versions - Latest release: 5 months ago - 13.8 thousand downloads total - 76 stars on GitHub - 1 maintainer
methrix 1.22.1
Fast and efficient summarization of generic bedGraph files from Bisufite sequencing6 versions - Latest release: 3 months ago - 1 dependent package - 11.8 thousand downloads total - 33 stars on GitHub - 1 maintainer
vissE 1.16.0
Visualising Set Enrichment Analysis Results5 versions - Latest release: 5 months ago - 9.45 thousand downloads total - 18 stars on GitHub - 1 maintainer
martini 1.28.0
GWAS Incorporating Networks5 versions - Latest release: 4 months ago - 12.7 thousand downloads total - 4 stars on GitHub - 1 maintainer
Top 2.4% on bioconductor.org
5 versions - Latest release: 4 months ago - 18 dependent packages - 575 thousand downloads total - 75 stars on GitHub - 1 maintainer
EBImage 4.50.0
Image processing and analysis toolbox for R5 versions - Latest release: 4 months ago - 18 dependent packages - 575 thousand downloads total - 75 stars on GitHub - 1 maintainer
ReducedExperiment 1.0.2
Containers and tools for dimensionally-reduced -omics representations2 versions - Latest release: 2 months ago - 1.74 thousand downloads total - 3 stars on GitHub - 1 maintainer
sevenbridges 1.38.0
Seven Bridges Platform API Client and Common Workflow Language Tool Builder in R5 versions - Latest release: 5 months ago - 19.3 thousand downloads total - 35 stars on GitHub - 1 maintainer
cogena 1.42.0
co-expressed gene-set enrichment analysis5 versions - Latest release: 4 months ago - 23.4 thousand downloads total - 12 stars on GitHub - 1 maintainer
GEOfastq 1.16.0
Downloads ENA Fastqs With GEO Accessions5 versions - Latest release: 4 months ago - 8.15 thousand downloads total - 4 stars on GitHub - 1 maintainer
epistack 1.14.0
Heatmaps of Stack Profiles from Epigenetic Signals5 versions - Latest release: 4 months ago - 6.76 thousand downloads total - 6 stars on GitHub - 1 maintainer
scMerge 1.24.0
scMerge: Merging multiple batches of scRNA-seq data5 versions - Latest release: 4 months ago - 2 dependent packages - 35.2 thousand downloads total - 67 stars on GitHub - 1 maintainer
cmapR 1.20.0
CMap Tools in R5 versions - Latest release: 4 months ago - 34.4 thousand downloads total - 93 stars on GitHub - 1 maintainer
biobtreeR 1.20.0
Using biobtree tool from R5 versions - Latest release: 4 months ago - 10.6 thousand downloads total - 3 stars on GitHub - 1 maintainer
ggseqalign 1.2.0
Minimal Visualization of Sequence Alignments2 versions - Latest release: 4 months ago - 2.37 thousand downloads total - 0 stars on GitHub - 1 maintainer
rTRM 1.46.0
Identification of Transcriptional Regulatory Modules from Protein-Protein Interaction Networks5 versions - Latest release: 5 months ago - 1 dependent package - 26 thousand downloads total - 3 stars on GitHub - 1 maintainer
BgeeDB 2.34.0
Annotation and gene expression data retrieval from Bgee database. TopAnat, an anatomical entities...6 versions - Latest release: 3 months ago - 2 dependent packages - 24.7 thousand downloads total - 16 stars on GitHub - 4 maintainers
methylInheritance 1.32.0
Permutation-Based Analysis associating Conserved Differentially Methylated Elements Across Multip...5 versions - Latest release: 5 months ago - 1 dependent package - 14.7 thousand downloads total - 0 stars on GitHub - 1 maintainer
TDbasedUFEadv 1.8.1
Advanced package of tensor decomposition based unsupervised feature extraction6 versions - Latest release: about 2 months ago - 5.6 thousand downloads total - 0 stars on GitHub - 1 maintainer
netSmooth 1.28.0
Network smoothing for scRNAseq5 versions - Latest release: 5 months ago - 1 dependent package - 13.6 thousand downloads total - 28 stars on GitHub - 1 maintainer
tidytof 1.2.0
Analyze High-dimensional Cytometry Data Using Tidy Data Principles2 versions - Latest release: 4 months ago - 2.34 thousand downloads total - 19 stars on GitHub - 1 maintainer
Top 4.1% on bioconductor.org
8 versions - Latest release: 2 months ago - 3 dependent packages - 207 thousand downloads total - 89 stars on GitHub - 1 maintainer
GenomicDataCommons 1.32.1
NIH / NCI Genomic Data Commons Access8 versions - Latest release: 2 months ago - 3 dependent packages - 207 thousand downloads total - 89 stars on GitHub - 1 maintainer
geneXtendeR 1.34.0
Optimized Functional Annotation Of ChIP-seq Data5 versions - Latest release: 4 months ago - 18.6 thousand downloads total - 9 stars on GitHub - 1 maintainer
Top 2.9% on bioconductor.org
6 versions - Latest release: 2 months ago - 8 dependent packages - 108 thousand downloads total - 337 stars on GitHub - 1 maintainer
karyoploteR 1.34.2
Plot customizable linear genomes displaying arbitrary data6 versions - Latest release: 2 months ago - 8 dependent packages - 108 thousand downloads total - 337 stars on GitHub - 1 maintainer
ClustIRR 1.6.0
Clustering of immune receptor repertoires4 versions - Latest release: 4 months ago - 4.63 thousand downloads total - 3 stars on GitHub - 1 maintainer
cfDNAPro 1.14.0
cfDNAPro extracts and Visualises biological features from whole genome sequencing data of cell-fr...5 versions - Latest release: 4 months ago - 8.27 thousand downloads total - 34 stars on GitHub - 1 maintainer
HIBAG 1.44.0
HLA Genotype Imputation with Attribute Bagging7 versions - Latest release: 4 months ago - 27.5 thousand downloads total - 28 stars on GitHub - 1 maintainer
TDbasedUFE 1.8.0
Tensor Decomposition Based Unsupervised Feature Extraction5 versions - Latest release: 4 months ago - 1 dependent package - 5.48 thousand downloads total - 5 stars on GitHub - 1 maintainer
CopyNumberPlots 1.24.0
Create Copy-Number Plots using karyoploteR functionality6 versions - Latest release: 3 months ago - 2 dependent packages - 14.2 thousand downloads total - 6 stars on GitHub - 1 maintainer
NormalyzerDE 1.26.0
Evaluation of normalization methods and calculation of differential expression analysis statistics5 versions - Latest release: 4 months ago - 19 thousand downloads total - 24 stars on GitHub - 1 maintainer
Top 3.6% on bioconductor.org
15 versions - Latest release: 25 days ago - 11 dependent packages - 114 thousand downloads total - 46 stars on GitHub - 1 maintainer
SeqArray 1.48.1
Data management of large-scale whole-genome sequence variant calls using GDS files15 versions - Latest release: 25 days ago - 11 dependent packages - 114 thousand downloads total - 46 stars on GitHub - 1 maintainer
decontam 1.28.0
Identify Contaminants in Marker-gene and Metagenomics Sequencing Data5 versions - Latest release: 4 months ago - 1 dependent package - 94.6 thousand downloads total - 160 stars on GitHub - 1 maintainer
Top 3.5% on bioconductor.org
5 versions - Latest release: 4 months ago - 2 dependent packages - 795 thousand downloads total - 502 stars on GitHub - 1 maintainer
dada2 1.36.0
Accurate, high-resolution sample inference from amplicon sequencing data5 versions - Latest release: 4 months ago - 2 dependent packages - 795 thousand downloads total - 502 stars on GitHub - 1 maintainer
rRDP 1.42.0
Interface to the RDP Classifier5 versions - Latest release: 4 months ago - 19.2 thousand downloads total - 3 stars on GitHub - 1 maintainer
rBLAST 1.4.0
R Interface for the Basic Local Alignment Search Tool3 versions - Latest release: 4 months ago - 6.33 thousand downloads total - 111 stars on GitHub - 1 maintainer
koinar 1.2.0
KoinaR - Remote machine learning inference using Koina3 versions - Latest release: 5 months ago - 2.32 thousand downloads total - 42 stars on GitHub - 1 maintainer
cTRAP 1.26.0
Identification of candidate causal perturbations from differential gene expression data6 versions - Latest release: 5 months ago - 11.8 thousand downloads total - 5 stars on GitHub - 1 maintainer
CiteFuse 1.20.0
CiteFuse: multi-modal analysis of CITE-seq data5 versions - Latest release: 4 months ago - 1 dependent package - 11.5 thousand downloads total - 25 stars on GitHub - 1 maintainer
mimager 1.32.0
mimager: The Microarray Imager5 versions - Latest release: 4 months ago - 13.8 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 6.8% on bioconductor.org
5 versions - Latest release: 4 months ago - 3 dependent packages - 101 thousand downloads total - 45 stars on GitHub - 1 maintainer
singscore 1.28.0
Rank-based single-sample gene set scoring method5 versions - Latest release: 4 months ago - 3 dependent packages - 101 thousand downloads total - 45 stars on GitHub - 1 maintainer
BERT 1.4.0
High Performance Data Integration for Large-Scale Analyses of Incomplete Omic Profiles Using Batc...3 versions - Latest release: 4 months ago - 3.53 thousand downloads total - 3 stars on GitHub - 1 maintainer
Top 2.7% on bioconductor.org
9 versions - Latest release: 26 days ago - 18 dependent packages - 263 thousand downloads total - 20 stars on GitHub - 1 maintainer
gdsfmt 1.44.1
R Interface to CoreArray Genomic Data Structure (GDS) Files9 versions - Latest release: 26 days ago - 18 dependent packages - 263 thousand downloads total - 20 stars on GitHub - 1 maintainer
Top 5.5% on bioconductor.org
5 versions - Latest release: 4 months ago - 6 dependent packages - 53.7 thousand downloads total - 205 stars on GitHub - 1 maintainer
splatter 1.32.0
Simple Simulation of Single-cell RNA Sequencing Data5 versions - Latest release: 4 months ago - 6 dependent packages - 53.7 thousand downloads total - 205 stars on GitHub - 1 maintainer
scruff 1.26.0
Single Cell RNA-Seq UMI Filtering Facilitator (scruff)5 versions - Latest release: 4 months ago - 12.3 thousand downloads total - 8 stars on GitHub - 1 maintainer
orthogene 1.14.0
Interspecies gene mapping5 versions - Latest release: 4 months ago - 1 dependent package - 20.9 thousand downloads total - 44 stars on GitHub - 1 maintainer
signeR 2.10.0
Empirical Bayesian approach to mutational signature discovery5 versions - Latest release: 4 months ago - 19.2 thousand downloads total - 13 stars on GitHub - 1 maintainer
PhyloProfile 2.0.6
PhyloProfile15 versions - Latest release: about 2 months ago - 12.3 thousand downloads total - 35 stars on GitHub - 1 maintainer
DEWSeq 1.22.0
Differential Expressed Windows Based on Negative Binomial Distribution5 versions - Latest release: 4 months ago - 9.72 thousand downloads total - 5 stars on GitHub - 1 maintainer
CellBench 1.24.0
Construct Benchmarks for Single Cell Analysis Methods5 versions - Latest release: 5 months ago - 2 dependent packages - 14.4 thousand downloads total - 31 stars on GitHub - 1 maintainer
miaDash 1.0.0
Shiny app for the interactive analysis and exploration of microbiome data1 version - Latest release: 5 months ago - 1.21 thousand downloads total - 1 stars on GitHub - 1 maintainer
packFinder 1.20.0
de novo Annotation of Pack-TYPE Transposable Elements5 versions - Latest release: 4 months ago - 8.87 thousand downloads total - 7 stars on GitHub - 1 maintainer
RandomWalkRestartMH 1.26.0 removed
Random walk with restart on multiplex and heterogeneous Networks4 versions - Latest release: 9 months ago - 1 dependent package - 10.7 thousand downloads total - 21 stars on GitHub - 1 maintainer
deco 1.18.0 removed
Decomposing Heterogeneous Cohorts using Omic Data Profiling2 versions - Latest release: almost 2 years ago - 4.59 thousand downloads total - 4 stars on GitHub - 1 maintainer
chromswitch 1.22.0 removed
An R package to detect chromatin state switches from epigenomic data1 version - Latest release: almost 2 years ago - 7.34 thousand downloads total - 3 stars on GitHub - 1 maintainer
RLSeq 1.6.0 removed
RLSeq: An analysis package for R-loop mapping data3 versions - Latest release: almost 2 years ago - 2.67 thousand downloads total - 2 stars on GitHub - 1 maintainer
Related Keywords
Software
73
r
33
bioconductor
25
Sequencing
23
GeneExpression
21
DataImport
17
Visualization
17
SingleCell
12
Network
12
genomics
12
ImmunoOncology
11
RNASeq
11
Genetics
10
Infrastructure
10
GeneSetEnrichment
9
Classification
9
Preprocessing
9
Clustering
8
Transcriptomics
8
Pathways
8
rstats
8
r-package
7
GraphAndNetwork
7
Microarray
6
single-cell
6
DataRepresentation
6
bioconductor-package
6
StatisticalMethod
6
Coverage
6
DifferentialExpression
5
DimensionReduction
5
Bayesian
5
Normalization
5
Annotation
5
FeatureExtraction
5
data-science
4
MultipleComparison
4
Microbiome
4
BatchEffect
4
BiomedicalInformatics
4
NetworkEnrichment
4
SystemsBiology
4
WholeGenome
4
GO
4
ThirdPartyClient
4
Alignment
4
Proteomics
4
FunctionalGenomics
4
QualityControl
4
scrna-seq
3
computational-biology
3
Epigenetics
3
snp
3
microbiome
3
gds-format
3
SequenceMatching
3
rna-seq
3
SomaticMutation
3
DNASeq
3
genomics-visualization
3
pathways
3
networks
3
visualization
3
Metabolomics
3
ComparativeGenomics
3
Transcription
3
dna-methylation
3
ChIPSeq
3
KEGG
3
OneChannel
3
DNAMethylation
3
proteomics
3
Reactome
3
MethylationArray
3
gwas
2
SNP
2
DifferentialPeakCalling
2
GenomicVariation
2
api-client
2
HistoneModification
2
GenomeWideAssociation
2
CopyNumberVariation
2
gene-expression
2
chip-seq
2
Phylogenetics
2
comparative-genomics
2
systems-biology
2
MathematicalBiology
2
tensor-decomposition
2
MethylSeq
2
mRNAMicroarray
2
clustering
2
Metagenomics
2
cmap
2
amplicon
2
metagenomics
2
GeneRegulation
2
metabarcoding
2
machine-learning
2
transcriptomics
2