bioconductor.org "FunctionalGenomics" keyword
View the packages on the bioconductor.org package registry that are tagged with the "FunctionalGenomics" keyword.
multistateQTL 2.2.0
Toolkit for the analysis of multi-state QTL data5 versions - Latest release: about 2 months ago - 4.55 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 0.6% on bioconductor.org
26 versions - Latest release: 8 days ago - 181 dependent packages - 4.18 million downloads total - 4 maintainers
edgeR 4.8.2
Empirical Analysis of Digital Gene Expression Data in R26 versions - Latest release: 8 days ago - 181 dependent packages - 4.18 million downloads total - 4 maintainers
Top 0.3% on bioconductor.org
16 versions - Latest release: 2 months ago - 322 dependent packages - 6.83 million downloads total - 1 maintainer
limma 3.66.0
Linear Models for Microarray and Omics Data16 versions - Latest release: 2 months ago - 322 dependent packages - 6.83 million downloads total - 1 maintainer
Top 1.5% on bioconductor.org
6 versions - Latest release: 2 months ago - 9 dependent packages - 327 thousand downloads total - 481 stars on GitHub - 1 maintainer
maftools 2.26.0 💰
Summarize, Analyze and Visualize MAF Files6 versions - Latest release: 2 months ago - 9 dependent packages - 327 thousand downloads total - 481 stars on GitHub - 1 maintainer
Top 2.4% on bioconductor.org
6 versions - Latest release: about 1 month ago - 2 dependent packages - 299 thousand downloads total - 1 maintainer
DiffBind 3.20.0
Differential Binding Analysis of ChIP-Seq Peak Data6 versions - Latest release: about 1 month ago - 2 dependent packages - 299 thousand downloads total - 1 maintainer
zenith 1.12.0
Gene set analysis following differential expression using linear (mixed) modeling with dream7 versions - Latest release: about 1 month ago - 2 dependent packages - 11.1 thousand downloads total - 0 stars on GitHub - 1 maintainer
epidecodeR 1.18.0
epidecodeR: a functional exploration tool for epigenetic and epitranscriptomic regulation6 versions - Latest release: 2 months ago - 8.09 thousand downloads total - 3 stars on GitHub - 1 maintainer
crumblr 1.2.0
Count ratio uncertainty modeling base linear regression2 versions - Latest release: about 2 months ago - 2.26 thousand downloads total - 6 stars on GitHub - 1 maintainer
HiCPotts 1.0.0
HiCPotts: Hierarchical Modeling to Identify and Correct Genomic Biases in Hi-C1 version - Latest release: 2 months ago - 799 downloads total - 0 stars on GitHub - 1 maintainer
mariner 1.10.0
Mariner: Explore the Hi-Cs7 versions - Latest release: about 1 month ago - 6.12 thousand downloads total - 1 maintainer
gDNAx 1.8.2
Diagnostics for assessing genomic DNA contamination in RNA-seq data11 versions - Latest release: 9 days ago - 5.85 thousand downloads total - 1 stars on GitHub - 1 maintainer
idr2d 1.24.0
Irreproducible Discovery Rate for Genomic Interactions Data7 versions - Latest release: about 1 month ago - 11.5 thousand downloads total - 1 maintainer
crisprViz 1.12.0
Visualization Functions for CRISPR gRNAs6 versions - Latest release: about 1 month ago - 2 dependent packages - 9.54 thousand downloads total - 9 stars on GitHub - 1 maintainer
crisprBowtie 1.14.0
Bowtie-based alignment of CRISPR gRNA spacer sequences6 versions - Latest release: about 1 month ago - 2 dependent packages - 12.3 thousand downloads total - 3 stars on GitHub - 1 maintainer
COCOA 2.24.0
Coordinate Covariation Analysis6 versions - Latest release: about 1 month ago - 14.2 thousand downloads total - 1 maintainer
Top 10.0% on bioconductor.org
6 versions - Latest release: about 1 month ago - 2 dependent packages - 45.6 thousand downloads total - 1 maintainer
CAGEr 2.16.0
Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcr...6 versions - Latest release: about 1 month ago - 2 dependent packages - 45.6 thousand downloads total - 1 maintainer
Cogito 1.16.0
Compare genomic intervals tool - Automated, complete, reproducible and clear report about genomic...6 versions - Latest release: about 1 month ago - 7.61 thousand downloads total - 1 maintainer
memes 1.18.0
motif matching, comparison, and de novo discovery using the MEME Suite6 versions - Latest release: about 1 month ago - 21.4 thousand downloads total - 43 stars on GitHub - 1 maintainer
BasicSTARRseq 1.38.0
Basic peak calling on STARR-seq data6 versions - Latest release: about 1 month ago - 19.4 thousand downloads total - 1 maintainer
Top 9.8% on bioconductor.org
6 versions - Latest release: about 1 month ago - 1 dependent package - 34.2 thousand downloads total - 1 maintainer
FGNet 3.44.0
Functional Gene Networks derived from biological enrichment analyses6 versions - Latest release: about 1 month ago - 1 dependent package - 34.2 thousand downloads total - 1 maintainer
TENET 1.2.0
R package for TENET (Tracing regulatory Element Networks using Epigenetic Traits) to identify key...3 versions - Latest release: about 1 month ago - 2.08 thousand downloads total - 1 stars on GitHub - 1 maintainer
screenCounter 1.10.0
Counting Reads in High-Throughput Sequencing Screens6 versions - Latest release: about 1 month ago - 5.83 thousand downloads total - 3 stars on GitHub - 1 maintainer
chipenrich 2.34.0
Gene Set Enrichment For ChIP-seq Peak Data6 versions - Latest release: about 1 month ago - 36.8 thousand downloads total - 1 maintainer
DEWSeq 1.24.0
Differential Expressed Windows Based on Negative Binomial Distribution6 versions - Latest release: about 2 months ago - 11.3 thousand downloads total - 5 stars on GitHub - 1 maintainer
sitadela 1.18.0
An R package for the easy provision of simple but complete tab-delimited genomic annotation from ...6 versions - Latest release: about 1 month ago - 7.74 thousand downloads total - 0 stars on GitHub - 1 maintainer
ModCon 1.18.0
Modifying splice site usage by changing the mRNP code, while maintaining the genetic code6 versions - Latest release: about 1 month ago - 7.15 thousand downloads total - 1 stars on GitHub - 1 maintainer
crisprDesign 1.12.0
Comprehensive design of CRISPR gRNAs for nucleases and base editors6 versions - Latest release: about 1 month ago - 3 dependent packages - 12.3 thousand downloads total - 24 stars on GitHub - 1 maintainer
sincell 1.42.0
R package for the statistical assessment of cell state hierarchies from single-cell RNA-seq data6 versions - Latest release: about 1 month ago - 22.6 thousand downloads total - 1 maintainer
spatzie 1.15.1
Identification of enriched motif pairs from chromatin interaction data6 versions - Latest release: about 1 month ago - 6.89 thousand downloads total - 1 maintainer
SurfR 1.6.0
Surface Protein Prediction and Identification10 versions - Latest release: about 2 months ago - 4.98 thousand downloads total - 0 stars on GitHub - 1 maintainer
gCrisprTools 2.16.0
Suite of Functions for Pooled Crispr Screen QC and Analysis6 versions - Latest release: about 1 month ago - 18.4 thousand downloads total - 1 maintainer
BindingSiteFinder 2.8.0
Binding site defintion based on iCLIP data6 versions - Latest release: about 1 month ago - 8.43 thousand downloads total - 3 stars on GitHub - 1 maintainer
fCCAC 1.36.0
functional Canonical Correlation Analysis to evaluate Covariance between nucleic acid sequencing ...6 versions - Latest release: about 1 month ago - 16.3 thousand downloads total - 0 stars on GitHub - 1 maintainer
customProDB 1.49.0
Generate customized protein database from NGS data, with a focus on RNA-Seq data, for proteomics ...7 versions - Latest release: about 1 month ago - 32.8 thousand downloads total - 1 maintainer
pfamAnalyzeR 1.10.0
Identification of domain isotypes in pfam data6 versions - Latest release: about 1 month ago - 1 dependent package - 15 thousand downloads total - 1 stars on GitHub - 1 maintainer
scQTLtools 1.1.7
scQTLtools: an R/Bioconductor package for comprehensive identification and visualization of singl...4 versions - Latest release: about 1 month ago - 2.15 thousand downloads total - 0 stars on GitHub - 1 maintainer
GenomicOZone 1.24.0
Delineate outstanding genomic zones of differential gene activity6 versions - Latest release: about 1 month ago - 10.9 thousand downloads total - 1 maintainer
MouseFM 1.20.0
In-silico methods for genetic finemapping in inbred mice7 versions - Latest release: about 1 month ago - 11.4 thousand downloads total - 0 stars on GitHub - 1 maintainer
OMICsPCA 1.28.0
An R package for quantitative integration and analysis of multiple omics assays from heterogeneou...6 versions - Latest release: about 1 month ago - 15.8 thousand downloads total - 1 maintainer
dmrseq 1.30.0
Detection and inference of differentially methylated regions from Whole Genome Bisulfite Sequencing9 versions - Latest release: about 1 month ago - 1 dependent package - 33.3 thousand downloads total - 1 maintainer
cageminer 1.16.0
Candidate Gene Miner7 versions - Latest release: about 1 month ago - 8.37 thousand downloads total - 1 stars on GitHub - 1 maintainer
IsoformSwitchAnalyzeR 2.10.0
Identify, Annotate and Visualize Isoform Switches with Functional Consequences from both short- a...6 versions - Latest release: about 1 month ago - 48.4 thousand downloads total - 1 maintainer
variancePartition 1.40.1
Quantify and interpret drivers of variation in multilevel gene expression experiments12 versions - Latest release: 10 days ago - 4 dependent packages - 122 thousand downloads total - 10 stars on GitHub - 1 maintainer
MIRA 1.32.0
Methylation-Based Inference of Regulatory Activity6 versions - Latest release: about 1 month ago - 1 dependent package - 17.4 thousand downloads total - 1 maintainer
pathwayPCA 1.26.0
Integrative Pathway Analysis with Modern PCA Methodology and Gene Selection6 versions - Latest release: about 1 month ago - 1 dependent package - 14.4 thousand downloads total - 11 stars on GitHub - 1 maintainer
NetActivity 1.12.0
Compute gene set scores from a deep learning framework6 versions - Latest release: about 1 month ago - 6.36 thousand downloads total - 1 maintainer
Top 6.4% on bioconductor.org
6 versions - Latest release: about 1 month ago - 3 dependent packages - 65.3 thousand downloads total - 1 maintainer
hpar 1.52.0
Human Protein Atlas in R6 versions - Latest release: about 1 month ago - 3 dependent packages - 65.3 thousand downloads total - 1 maintainer
roastgsa 1.8.0
Rotation based gene set analysis5 versions - Latest release: about 1 month ago - 5.24 thousand downloads total - 0 stars on GitHub - 1 maintainer
RITAN 1.34.0
Rapid Integration of Term Annotation and Network resources6 versions - Latest release: about 1 month ago - 15.2 thousand downloads total - 1 maintainer
nullranges 1.16.3
Generation of null ranges via bootstrapping or covariate matching7 versions - Latest release: 10 days ago - 1 dependent package - 14.8 thousand downloads total - 22 stars on GitHub - 1 maintainer
plotgardener 1.16.0
Coordinate-Based Genomic Visualization Package for R11 versions - Latest release: about 1 month ago - 4 dependent packages - 21 thousand downloads total - 335 stars on GitHub - 2 maintainers
MOMA 1.22.0
Multi Omic Master Regulator Analysis6 versions - Latest release: about 1 month ago - 10.2 thousand downloads total - 5 stars on GitHub - 1 maintainer
metaseqR2 1.22.0
An R package for the analysis and result reporting of RNA-Seq data by combining multiple statisti...6 versions - Latest release: about 1 month ago - 11.5 thousand downloads total - 1 maintainer
chromPlot 1.38.0
Global visualization tool of genomic data6 versions - Latest release: about 1 month ago - 24.3 thousand downloads total - 1 maintainer
Top 6.8% on bioconductor.org
6 versions - Latest release: about 1 month ago - 6 dependent packages - 88.7 thousand downloads total - 25 stars on GitHub - 1 maintainer
annotatr 1.36.0
Annotation of Genomic Regions to Genomic Annotations6 versions - Latest release: about 1 month ago - 6 dependent packages - 88.7 thousand downloads total - 25 stars on GitHub - 1 maintainer
ncRNAtools 1.20.0
An R toolkit for non-coding RNA6 versions - Latest release: about 1 month ago - 8.8 thousand downloads total - 1 stars on GitHub - 1 maintainer
ORFik 1.30.2
Open Reading Frames in Genomics13 versions - Latest release: 10 days ago - 2 dependent packages - 30.7 thousand downloads total - 34 stars on GitHub - 1 maintainer
EGAD 1.38.0
Extending guilt by association by degree6 versions - Latest release: about 1 month ago - 21.1 thousand downloads total - 1 maintainer
cogeqc 1.14.0
Systematic quality checks on comparative genomics analyses7 versions - Latest release: about 2 months ago - 8.07 thousand downloads total - 8 stars on GitHub - 1 maintainer
HybridExpress 1.6.0
Comparative analysis of RNA-seq data for hybrids and their progenitors5 versions - Latest release: about 1 month ago - 5.03 thousand downloads total - 14 stars on GitHub - 1 maintainer
MotifPeeker 1.2.0
Benchmarking Epigenomic Profiling Methods Using Motif Enrichment2 versions - Latest release: about 1 month ago - 2.5 thousand downloads total - 2 stars on GitHub - 1 maintainer
crisprBase 1.14.0
Base functions and classes for CRISPR gRNA design6 versions - Latest release: about 1 month ago - 6 dependent packages - 12.6 thousand downloads total - 5 stars on GitHub - 1 maintainer
miloR 2.6.0
Differential neighbourhood abundance testing on a graph7 versions - Latest release: about 2 months ago - 42.4 thousand downloads total - 398 stars on GitHub - 1 maintainer
Top 6.0% on bioconductor.org
13 versions - Latest release: 10 days ago - 3 dependent packages - 174 thousand downloads total - 67 stars on GitHub - 1 maintainer
tximeta 1.28.1
Transcript Quantification Import with Automatic Metadata13 versions - Latest release: 10 days ago - 3 dependent packages - 174 thousand downloads total - 67 stars on GitHub - 1 maintainer
proActiv 1.20.0
Estimate Promoter Activity from RNA-Seq data6 versions - Latest release: about 2 months ago - 11.3 thousand downloads total - 53 stars on GitHub - 1 maintainer
Top 2.2% on bioconductor.org
17 versions - Latest release: 10 days ago - 15 dependent packages - 719 thousand downloads total - 227 stars on GitHub - 1 maintainer
GSVA 2.4.4
Gene Set Variation Analysis for Microarray and RNA-Seq Data17 versions - Latest release: 10 days ago - 15 dependent packages - 719 thousand downloads total - 227 stars on GitHub - 1 maintainer
CexoR 1.48.0
An R package to uncover high-resolution protein-DNA interactions in ChIP-exo replicates6 versions - Latest release: about 2 months ago - 25.8 thousand downloads total - 0 stars on GitHub - 1 maintainer
atena 1.16.1
Analysis of Transposable Elements8 versions - Latest release: 10 days ago - 11.3 thousand downloads total - 13 stars on GitHub - 1 maintainer
doubletrouble 1.10.0
Identification and classification of duplicated genes13 versions - Latest release: about 1 month ago - 7.41 thousand downloads total - 28 stars on GitHub - 1 maintainer
MIRit 1.6.1
Integrate microRNA and gene expression to decipher pathway complexity8 versions - Latest release: 10 days ago - 5.34 thousand downloads total - 1 stars on GitHub - 1 maintainer
GenomicDistributions 1.18.0
GenomicDistributions: fast analysis of genomic intervals with Bioconductor6 versions - Latest release: about 1 month ago - 11.4 thousand downloads total - 1 maintainer
dreamlet 1.8.0
Scalable differential expression analysis of single cell transcriptomics datasets with complex st...7 versions - Latest release: about 2 months ago - 7.93 thousand downloads total - 20 stars on GitHub - 1 maintainer
crisprScore 1.14.0
On-Target and Off-Target Scoring Algorithms for CRISPR gRNAs6 versions - Latest release: about 1 month ago - 3 dependent packages - 13.1 thousand downloads total - 11 stars on GitHub - 1 maintainer
loci2path 1.30.0
Loci2path: regulatory annotation of genomic intervals based on tissue-specific expression QTLs6 versions - Latest release: about 2 months ago - 12.9 thousand downloads total - 1 stars on GitHub - 1 maintainer
ISAnalytics 1.20.0
Analyze gene therapy vector insertion sites data identified from genomics next generation sequenc...7 versions - Latest release: about 1 month ago - 9.19 thousand downloads total - 3 stars on GitHub - 1 maintainer
sevenC 1.30.0
Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs6 versions - Latest release: about 1 month ago - 14 thousand downloads total - 13 stars on GitHub - 1 maintainer
crisprVerse 1.12.0
Easily install and load the crisprVerse ecosystem for CRISPR gRNA design6 versions - Latest release: about 2 months ago - 8.72 thousand downloads total - 7 stars on GitHub - 1 maintainer
EWCE 1.18.0
Expression Weighted Celltype Enrichment7 versions - Latest release: about 1 month ago - 19.6 thousand downloads total - 53 stars on GitHub - 1 maintainer
QTLExperiment 2.2.0
S4 classes for QTL summary statistics and metadata5 versions - Latest release: about 2 months ago - 1 dependent package - 5.46 thousand downloads total - 2 stars on GitHub - 1 maintainer
crisprBwa 1.14.0
BWA-based alignment of CRISPR gRNA spacer sequences6 versions - Latest release: about 2 months ago - 1 dependent package - 7.91 thousand downloads total - 1 stars on GitHub - 1 maintainer
planttfhunter 1.10.0
Identification and classification of plant transcription factors6 versions - Latest release: about 2 months ago - 5.94 thousand downloads total - 1 stars on GitHub - 1 maintainer
syntenet 1.12.0
Inference And Analysis Of Synteny Networks10 versions - Latest release: about 2 months ago - 1 dependent package - 9.9 thousand downloads total - 33 stars on GitHub - 1 maintainer
RIVER 1.34.0
R package for RIVER (RNA-Informed Variant Effect on Regulation)6 versions - Latest release: about 2 months ago - 15.1 thousand downloads total - 10 stars on GitHub - 1 maintainer
GenomAutomorphism 1.12.0
Compute the automorphisms between DNA's Abelian group representations7 versions - Latest release: about 2 months ago - 6.66 thousand downloads total - 0 stars on GitHub - 1 maintainer
airpart 1.18.0
Differential cell-type-specific allelic imbalance6 versions - Latest release: about 2 months ago - 10.8 thousand downloads total - 2 stars on GitHub - 1 maintainer
DepInfeR 1.14.0
Inferring tumor-specific cancer dependencies through integrating ex-vivo drug response assays and...6 versions - Latest release: about 2 months ago - 6.57 thousand downloads total - 0 stars on GitHub - 1 maintainer
mpra 1.32.0
Analyze massively parallel reporter assays8 versions - Latest release: about 2 months ago - 15.8 thousand downloads total - 6 stars on GitHub - 1 maintainer
preciseTAD 1.20.0
preciseTAD: A machine learning framework for precise TAD boundary prediction6 versions - Latest release: about 2 months ago - 10.9 thousand downloads total - 8 stars on GitHub - 1 maintainer
LOLA 1.39.1
Locus overlap analysis for enrichment of genomic ranges6 versions - Latest release: about 2 months ago - 5 dependent packages - 40.1 thousand downloads total - 1 maintainer
OmaDB 2.26.0
R wrapper for the OMA REST API6 versions - Latest release: about 2 months ago - 2 dependent packages - 19.5 thousand downloads total - 2 stars on GitHub - 2 maintainers
crisprShiny 1.6.0
Exploring curated CRISPR gRNAs via Shiny4 versions - Latest release: about 2 months ago - 4.33 thousand downloads total - 2 stars on GitHub - 1 maintainer
eisaR 1.22.1
Exon-Intron Split Analysis (EISA) in R7 versions - Latest release: about 2 months ago - 15.6 thousand downloads total - 16 stars on GitHub - 1 maintainer
rigvf 1.2.2
R interface to the IGVF Catalog4 versions - Latest release: 18 days ago - 2.3 thousand downloads total - 0 stars on GitHub - 1 maintainer
decoupleR 2.16.0
decoupleR: Ensemble of computational methods to infer biological activities from omics data7 versions - Latest release: about 2 months ago - 3 dependent packages - 75.3 thousand downloads total - 268 stars on GitHub - 1 maintainer
rfaRm 1.22.0
An R interface to the Rfam database8 versions - Latest release: about 2 months ago - 9.59 thousand downloads total - 2 maintainers
AlphaMissenseR 1.6.1
Accessing AlphaMissense Data Resources in R8 versions - Latest release: 22 days ago - 5.37 thousand downloads total - 9 stars on GitHub - 1 maintainer
AlphaBeta 1.24.0
Computational inference of epimutation rates and spectra from high-throughput DNA methylation dat...6 versions - Latest release: about 2 months ago - 14.5 thousand downloads total - 1 maintainer
goatea 1.0.0
Interactive Exploration of GSEA by the GOAT Method1 version - Latest release: 2 months ago - 111 downloads total - 1 maintainer
VarCon 1.18.0
VarCon: an R package for retrieving neighboring nucleotides of an SNV6 versions - Latest release: about 2 months ago - 7.69 thousand downloads total - 1 maintainer
EpiCompare 1.14.0
Comparison, Benchmarking & QC of Epigenomic Datasets15 versions - Latest release: about 1 month ago - 6.37 thousand downloads total - 17 stars on GitHub - 1 maintainer
Related Keywords
Software
109
Sequencing
37
GeneExpression
35
RNASeq
30
Transcription
28
Epigenetics
28
Visualization
26
SystemsBiology
25
GeneRegulation
25
DifferentialExpression
25
Transcriptomics
24
GeneSetEnrichment
22
ImmunoOncology
20
Genetics
20
Regression
20
BiomedicalInformatics
19
DataImport
19
MultipleComparison
18
ChIPSeq
17
QualityControl
15
Preprocessing
15
Clustering
15
Normalization
14
FunctionalPrediction
14
Coverage
13
CellBiology
13
Annotation
13
AlternativeSplicing
12
Pathways
11
GenomeAnnotation
11
Classification
11
CRISPR
11
Network
11
bioconductor
10
SNP
10
BatchEffect
10
GeneTarget
10
SingleCell
10
Microarray
9
Proteomics
9
bioconductor-package
9
crispr-design
8
crispr
8
GenomicVariation
8
Alignment
7
genomics
7
GenePrediction
7
ATACSeq
7
PeakDetection
7
NetworkEnrichment
7
Bayesian
7
DNAMethylation
7
grna
7
grna-sequence
7
grna-sequences
7
HiC
6
crispr-target
6
GenomeWideAssociation
6
ComparativeGenomics
6
MethylSeq
6
HistoneModification
6
DifferentialSplicing
6
DifferentialMethylation
6
GraphAndNetwork
5
sgrna
5
GO
5
crispr-analysis
5
sgrna-design
5
crispr-cas9
5
rstats
5
r
5
DataRepresentation
5
FeatureExtraction
5
VariantAnnotation
5
r-package
4
TimeCourse
4
NetworkInference
4
WholeGenome
4
Survival
4
bioinformatics
4
MathematicalBiology
4
GeneticVariability
4
PrincipalComponent
4
TranscriptomeVariant
4
DNaseSeq
4
WorkflowStep
3
Pharmacogenetics
3
chip-seq
3
transcriptomics
3
comparative-genomics
3
Phylogenetics
3
ThirdPartyClient
3
GenomeAssembly
3
Pharmacogenomics
3
SequenceMatching
3
GUI
3
MethylationArray
3
DNA3DStructure
3
DifferentialPeakCalling
3
mRNAMicroarray
3