bioconductor.org "FunctionalGenomics" keyword
View the packages on the bioconductor.org package registry that are tagged with the "FunctionalGenomics" keyword.
Top 0.3% on bioconductor.org
14 versions - Latest release: 2 months ago - 322 dependent packages - 5.97 million downloads total - 1 maintainer
limma 3.64.1
Linear Models for Microarray and Omics Data14 versions - Latest release: 2 months ago - 322 dependent packages - 5.97 million downloads total - 1 maintainer
crumblr 1.0.0
Count ratio uncertainty modeling base linear regression1 version - Latest release: 3 months ago - 1.15 thousand downloads total - 6 stars on GitHub - 1 maintainer
rigvf 1.0.2
R interface to the IGVF Catalog2 versions - Latest release: about 1 month ago - 1.21 thousand downloads total - 0 stars on GitHub - 1 maintainer
loci2path 1.28.0
Loci2path: regulatory annotation of genomic intervals based on tissue-specific expression QTLs5 versions - Latest release: 3 months ago - 11.4 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 1.5% on bioconductor.org
5 versions - Latest release: 3 months ago - 9 dependent packages - 281 thousand downloads total - 469 stars on GitHub - 1 maintainer
maftools 2.24.0 💰
Summarize, Analyze and Visualize MAF Files5 versions - Latest release: 3 months ago - 9 dependent packages - 281 thousand downloads total - 469 stars on GitHub - 1 maintainer
Top 0.6% on bioconductor.org
23 versions - Latest release: 16 days ago - 181 dependent packages - 3.6 million downloads total - 4 maintainers
edgeR 4.6.3
Empirical Analysis of Digital Gene Expression Data in R23 versions - Latest release: 16 days ago - 181 dependent packages - 3.6 million downloads total - 4 maintainers
Top 6.8% on bioconductor.org
5 versions - Latest release: 3 months ago - 6 dependent packages - 71.8 thousand downloads total - 25 stars on GitHub - 1 maintainer
annotatr 1.34.0
Annotation of Genomic Regions to Genomic Annotations5 versions - Latest release: 3 months ago - 6 dependent packages - 71.8 thousand downloads total - 25 stars on GitHub - 1 maintainer
MotifPeeker 1.0.0
Benchmarking Epigenomic Profiling Methods Using Motif Enrichment1 version - Latest release: 3 months ago - 1.48 thousand downloads total - 2 stars on GitHub - 1 maintainer
nullranges 1.14.0
Generation of null ranges via bootstrapping or covariate matching5 versions - Latest release: 2 months ago - 1 dependent package - 11 thousand downloads total - 22 stars on GitHub - 1 maintainer
crisprVerse 1.10.0
Easily install and load the crisprVerse ecosystem for CRISPR gRNA design5 versions - Latest release: 3 months ago - 7.08 thousand downloads total - 7 stars on GitHub - 1 maintainer
crisprScore 1.12.0
On-Target and Off-Target Scoring Algorithms for CRISPR gRNAs5 versions - Latest release: 3 months ago - 3 dependent packages - 10.7 thousand downloads total - 11 stars on GitHub - 1 maintainer
epidecodeR 1.16.0
epidecodeR: a functional exploration tool for epigenetic and epitranscriptomic regulation5 versions - Latest release: 3 months ago - 6.74 thousand downloads total - 3 stars on GitHub - 1 maintainer
screenCounter 1.8.0
Counting Reads in High-Throughput Sequencing Screens5 versions - Latest release: 2 months ago - 4.57 thousand downloads total - 3 stars on GitHub - 1 maintainer
RIVER 1.32.0
R package for RIVER (RNA-Informed Variant Effect on Regulation)5 versions - Latest release: 3 months ago - 13.5 thousand downloads total - 10 stars on GitHub - 1 maintainer
scQTLtools 1.0.3
An R package for single-cell eQTL analysis and visualization3 versions - Latest release: about 1 month ago - 1.44 thousand downloads total - 0 stars on GitHub - 1 maintainer
memes 1.16.0
motif matching, comparison, and de novo discovery using the MEME Suite5 versions - Latest release: 3 months ago - 17.2 thousand downloads total - 43 stars on GitHub - 1 maintainer
proActiv 1.18.0
Estimate Promoter Activity from RNA-Seq data5 versions - Latest release: 2 months ago - 8.72 thousand downloads total - 53 stars on GitHub - 1 maintainer
sevenC 1.28.0
Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs5 versions - Latest release: 3 months ago - 12.1 thousand downloads total - 12 stars on GitHub - 1 maintainer
crisprBowtie 1.12.0
Bowtie-based alignment of CRISPR gRNA spacer sequences5 versions - Latest release: 2 months ago - 2 dependent packages - 9.97 thousand downloads total - 3 stars on GitHub - 1 maintainer
Top 6.0% on bioconductor.org
10 versions - Latest release: 2 months ago - 3 dependent packages - 123 thousand downloads total - 68 stars on GitHub - 1 maintainer
tximeta 1.26.1
Transcript Quantification Import with Automatic Metadata10 versions - Latest release: 2 months ago - 3 dependent packages - 123 thousand downloads total - 68 stars on GitHub - 1 maintainer
doubletrouble 1.8.0
Identification and classification of duplicated genes11 versions - Latest release: 3 months ago - 5.74 thousand downloads total - 27 stars on GitHub - 1 maintainer
cogeqc 1.12.0
Systematic quality checks on comparative genomics analyses6 versions - Latest release: 3 months ago - 6.54 thousand downloads total - 8 stars on GitHub - 1 maintainer
planttfhunter 1.8.0
Identification and classification of plant transcription factors5 versions - Latest release: 2 months ago - 4.67 thousand downloads total - 1 stars on GitHub - 1 maintainer
crisprDesign 1.10.0
Comprehensive design of CRISPR gRNAs for nucleases and base editors5 versions - Latest release: 3 months ago - 3 dependent packages - 9.71 thousand downloads total - 23 stars on GitHub - 1 maintainer
syntenet 1.10.0
Inference And Analysis Of Synteny Networks8 versions - Latest release: 3 months ago - 1 dependent package - 7.84 thousand downloads total - 30 stars on GitHub - 1 maintainer
GenomicDistributions 1.16.1
GenomicDistributions: fast analysis of genomic intervals with Bioconductor5 versions - Latest release: 3 months ago - 9.47 thousand downloads total - 1 maintainer
TENET 1.0.1
R package for TENET (Tracing regulatory Element Networks using Epigenetic Traits) to identify key...2 versions - Latest release: about 2 months ago - 937 downloads total - 1 stars on GitHub - 1 maintainer
variancePartition 1.38.0
Quantify and interpret drivers of variation in multilevel gene expression experiments9 versions - Latest release: 3 months ago - 4 dependent packages - 84.2 thousand downloads total - 8 stars on GitHub - 1 maintainer
QTLExperiment 2.0.1
S4 classes for QTL summary statistics and metadata4 versions - Latest release: 3 months ago - 1 dependent package - 4.15 thousand downloads total - 2 stars on GitHub - 1 maintainer
atena 1.14.1
Analysis of Transposable Elements6 versions - Latest release: about 1 month ago - 9.75 thousand downloads total - 10 stars on GitHub - 1 maintainer
chromPlot 1.36.0
Global visualization tool of genomic data5 versions - Latest release: 3 months ago - 21.8 thousand downloads total - 1 maintainer
GenomAutomorphism 1.10.0
Compute the automorphisms between DNA's Abelian group representations6 versions - Latest release: 3 months ago - 5.23 thousand downloads total - 0 stars on GitHub - 1 maintainer
BindingSiteFinder 2.6.0
Binding site defintion based on iCLIP data5 versions - Latest release: 3 months ago - 6.69 thousand downloads total - 3 stars on GitHub - 1 maintainer
MouseFM 1.18.0
In-silico methods for genetic finemapping in inbred mice6 versions - Latest release: 3 months ago - 9.91 thousand downloads total - 0 stars on GitHub - 1 maintainer
MOMA 1.20.0
Multi Omic Master Regulator Analysis5 versions - Latest release: 3 months ago - 8.62 thousand downloads total - 5 stars on GitHub - 1 maintainer
multistateQTL 2.0.0
Toolkit for the analysis of multi-state QTL data4 versions - Latest release: 3 months ago - 3.22 thousand downloads total - 1 stars on GitHub - 1 maintainer
decoupleR 2.14.0
decoupleR: Ensemble of computational methods to infer biological activities from omics data6 versions - Latest release: 2 months ago - 3 dependent packages - 54.6 thousand downloads total - 256 stars on GitHub - 1 maintainer
idr2d 1.22.0
Irreproducible Discovery Rate for Genomic Interactions Data5 versions - Latest release: 3 months ago - 9.21 thousand downloads total - 1 maintainer
crisprBwa 1.12.0
BWA-based alignment of CRISPR gRNA spacer sequences5 versions - Latest release: 3 months ago - 1 dependent package - 6.33 thousand downloads total - 1 stars on GitHub - 1 maintainer
MIRit 1.4.1
Integrate microRNA and gene expression to decipher pathway complexity5 versions - Latest release: about 2 months ago - 3.69 thousand downloads total - 1 stars on GitHub - 1 maintainer
DepInfeR 1.12.0
Inferring tumor-specific cancer dependencies through integrating ex-vivo drug response assays and...5 versions - Latest release: 3 months ago - 5.13 thousand downloads total - 0 stars on GitHub - 1 maintainer
eisaR 1.20.0
Exon-Intron Split Analysis (EISA) in R6 versions - Latest release: 3 months ago - 12.8 thousand downloads total - 16 stars on GitHub - 1 maintainer
normr 1.34.0
Normalization and difference calling in ChIP-seq data5 versions - Latest release: 3 months ago - 20.6 thousand downloads total - 11 stars on GitHub - 1 maintainer
cageminer 1.14.0
Candidate Gene Miner5 versions - Latest release: 3 months ago - 6.48 thousand downloads total - 1 stars on GitHub - 1 maintainer
ORFik 1.28.2
Open Reading Frames in Genomics10 versions - Latest release: 3 months ago - 2 dependent packages - 22.6 thousand downloads total - 33 stars on GitHub - 1 maintainer
SurfR 1.4.1
Surface Protein Prediction and Identification8 versions - Latest release: 24 days ago - 3.48 thousand downloads total - 0 stars on GitHub - 1 maintainer
preciseTAD 1.18.0
preciseTAD: A machine learning framework for precise TAD boundary prediction5 versions - Latest release: 2 months ago - 7.45 thousand downloads total - 8 stars on GitHub - 1 maintainer
crisprViz 1.10.0
Visualization Functions for CRISPR gRNAs5 versions - Latest release: 3 months ago - 2 dependent packages - 7.44 thousand downloads total - 9 stars on GitHub - 1 maintainer
AlphaMissenseR 1.4.0
Accessing AlphaMissense Data Resources in R5 versions - Latest release: 3 months ago - 3.74 thousand downloads total - 8 stars on GitHub - 1 maintainer
CexoR 1.46.0
An R package to uncover high-resolution protein-DNA interactions in ChIP-exo replicates5 versions - Latest release: 3 months ago - 23.3 thousand downloads total - 0 stars on GitHub - 1 maintainer
rfaRm 1.20.0
An R interface to the Rfam database7 versions - Latest release: 3 months ago - 8 thousand downloads total - 2 maintainers
AlphaBeta 1.22.0
Computational inference of epimutation rates and spectra from high-throughput DNA methylation dat...5 versions - Latest release: 3 months ago - 12.7 thousand downloads total - 1 maintainer
LOLA 1.38.0
Locus overlap analysis for enrichment of genomic ranges5 versions - Latest release: 3 months ago - 5 dependent packages - 31.3 thousand downloads total - 1 maintainer
HybridExpress 1.4.0
Comparative analysis of RNA-seq data for hybrids and their progenitors4 versions - Latest release: 3 months ago - 3.62 thousand downloads total - 14 stars on GitHub - 1 maintainer
mpra 1.30.1
Analyze massively parallel reporter assays7 versions - Latest release: about 2 months ago - 13.1 thousand downloads total - 6 stars on GitHub - 1 maintainer
sitadela 1.16.0
An R package for the easy provision of simple but complete tab-delimited genomic annotation from ...5 versions - Latest release: 3 months ago - 6.11 thousand downloads total - 0 stars on GitHub - 1 maintainer
metaseqR2 1.20.0
An R package for the analysis and result reporting of RNA-Seq data by combining multiple statisti...5 versions - Latest release: 3 months ago - 9.37 thousand downloads total - 1 maintainer
IsoformSwitchAnalyzeR 2.8.0
Identify, Annotate and Visualize Isoform Switches with Functional Consequences from both short- a...5 versions - Latest release: 3 months ago - 37.7 thousand downloads total - 1 maintainer
gDNAx 1.6.1
Diagnostics for assessing genomic DNA contamination in RNA-seq data9 versions - Latest release: 29 days ago - 4.34 thousand downloads total - 1 stars on GitHub - 1 maintainer
zenith 1.10.0
Gene set analysis following differential expression using linear (mixed) modeling with dream6 versions - Latest release: 3 months ago - 2 dependent packages - 8.28 thousand downloads total - 0 stars on GitHub - 1 maintainer
RITAN 1.32.0
Rapid Integration of Term Annotation and Network resources5 versions - Latest release: 3 months ago - 13.4 thousand downloads total - 1 maintainer
BasicSTARRseq 1.36.0
Basic peak calling on STARR-seq data5 versions - Latest release: 3 months ago - 17.3 thousand downloads total - 1 maintainer
dmrseq 1.28.0
Detection and inference of differentially methylated regions from Whole Genome Bisulfite Sequencing8 versions - Latest release: 3 months ago - 1 dependent package - 26.8 thousand downloads total - 1 maintainer
Cogito 1.14.0
Compare genomic intervals tool - Automated, complete, reproducible and clear report about genomic...5 versions - Latest release: 3 months ago - 5.9 thousand downloads total - 1 maintainer
VarCon 1.16.0
VarCon: an R package for retrieving neighboring nucleotides of an SNV5 versions - Latest release: 3 months ago - 6.23 thousand downloads total - 1 maintainer
Top 2.2% on bioconductor.org
14 versions - Latest release: 3 months ago - 15 dependent packages - 554 thousand downloads total - 217 stars on GitHub - 1 maintainer
GSVA 2.2.0
Gene Set Variation Analysis for Microarray and RNA-Seq Data14 versions - Latest release: 3 months ago - 15 dependent packages - 554 thousand downloads total - 217 stars on GitHub - 1 maintainer
ModCon 1.16.0
Modifying splice site usage by changing the mRNP code, while maintaining the genetic code5 versions - Latest release: 3 months ago - 5.68 thousand downloads total - 1 stars on GitHub - 1 maintainer
OMICsPCA 1.26.0
An R package for quantitative integration and analysis of multiple omics assays from heterogeneou...5 versions - Latest release: 3 months ago - 11.3 thousand downloads total - 1 maintainer
spatzie 1.14.0
Identification of enriched motif pairs from chromatin interaction data5 versions - Latest release: 3 months ago - 5.65 thousand downloads total - 1 maintainer
Top 9.8% on bioconductor.org
5 versions - Latest release: 3 months ago - 1 dependent package - 31.8 thousand downloads total - 1 maintainer
FGNet 3.42.0
Functional Gene Networks derived from biological enrichment analyses5 versions - Latest release: 3 months ago - 1 dependent package - 31.8 thousand downloads total - 1 maintainer
NetActivity 1.10.0
Compute gene set scores from a deep learning framework5 versions - Latest release: 3 months ago - 4.86 thousand downloads total - 1 maintainer
crisprBase 1.12.0
Base functions and classes for CRISPR gRNA design5 versions - Latest release: 3 months ago - 6 dependent packages - 10 thousand downloads total - 5 stars on GitHub - 1 maintainer
OmaDB 2.24.0
R wrapper for the OMA REST API5 versions - Latest release: 3 months ago - 2 dependent packages - 16.8 thousand downloads total - 2 stars on GitHub - 2 maintainers
Top 2.4% on bioconductor.org
5 versions - Latest release: 3 months ago - 2 dependent packages - 266 thousand downloads total - 1 maintainer
DiffBind 3.18.0
Differential Binding Analysis of ChIP-Seq Peak Data5 versions - Latest release: 3 months ago - 2 dependent packages - 266 thousand downloads total - 1 maintainer
EGAD 1.36.0
Extending guilt by association by degree5 versions - Latest release: 3 months ago - 17.8 thousand downloads total - 1 maintainer
customProDB 1.48.0
Generate customized protein database from NGS data, with a focus on RNA-Seq data, for proteomics ...6 versions - Latest release: 3 months ago - 30.7 thousand downloads total - 1 maintainer
GenomicOZone 1.22.0
Delineate outstanding genomic zones of differential gene activity5 versions - Latest release: 3 months ago - 9.18 thousand downloads total - 1 maintainer
heatmaps 1.32.0
Flexible Heatmaps for Functional Genomics and Sequence Features5 versions - Latest release: 3 months ago - 1 dependent package - 34.7 thousand downloads total - 1 maintainer
pfamAnalyzeR 1.8.0
Identification of domain isotypes in pfam data5 versions - Latest release: 3 months ago - 1 dependent package - 11.9 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 10.0% on bioconductor.org
5 versions - Latest release: 3 months ago - 2 dependent packages - 39 thousand downloads total - 1 maintainer
CAGEr 2.14.0
Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcr...5 versions - Latest release: 3 months ago - 2 dependent packages - 39 thousand downloads total - 1 maintainer
Top 9.3% on bioconductor.org
5 versions - Latest release: 3 months ago - 1 dependent package - 40.5 thousand downloads total - 1 maintainer
MAGeCKFlute 2.12.0
Integrative Analysis Pipeline for Pooled CRISPR Functional Genetic Screens5 versions - Latest release: 3 months ago - 1 dependent package - 40.5 thousand downloads total - 1 maintainer
Top 6.4% on bioconductor.org
5 versions - Latest release: 3 months ago - 3 dependent packages - 60.8 thousand downloads total - 1 maintainer
hpar 1.50.0
Human Protein Atlas in R5 versions - Latest release: 3 months ago - 3 dependent packages - 60.8 thousand downloads total - 1 maintainer
airpart 1.16.0
Differential cell-type-specific allelic imbalance5 versions - Latest release: 3 months ago - 8.99 thousand downloads total - 2 stars on GitHub - 1 maintainer
gCrisprTools 2.14.0
Suite of Functions for Pooled Crispr Screen QC and Analysis5 versions - Latest release: 3 months ago - 15.9 thousand downloads total - 1 maintainer
crisprShiny 1.4.0
Exploring curated CRISPR gRNAs via Shiny3 versions - Latest release: 3 months ago - 3.24 thousand downloads total - 2 stars on GitHub - 1 maintainer
miloR 2.4.1
Differential neighbourhood abundance testing on a graph6 versions - Latest release: about 2 months ago - 24.7 thousand downloads total - 379 stars on GitHub - 1 maintainer
fCCAC 1.34.0
functional Canonical Correlation Analysis to evaluate Covariance between nucleic acid sequencing ...5 versions - Latest release: 3 months ago - 14 thousand downloads total - 0 stars on GitHub - 1 maintainer
COCOA 2.22.0
Coordinate Covariation Analysis5 versions - Latest release: 3 months ago - 11.2 thousand downloads total - 1 maintainer
chipenrich 2.32.0
Gene Set Enrichment For ChIP-seq Peak Data5 versions - Latest release: 3 months ago - 33.1 thousand downloads total - 1 maintainer
sincell 1.40.0
R package for the statistical assessment of cell state hierarchies from single-cell RNA-seq data5 versions - Latest release: 3 months ago - 20.1 thousand downloads total - 1 maintainer
MIRA 1.30.0
Methylation-Based Inference of Regulatory Activity5 versions - Latest release: 3 months ago - 1 dependent package - 14.5 thousand downloads total - 1 maintainer
ncRNAtools 1.18.0
An R toolkit for non-coding RNA5 versions - Latest release: 3 months ago - 7.05 thousand downloads total - 1 stars on GitHub - 1 maintainer
DEWSeq 1.22.0
Differential Expressed Windows Based on Negative Binomial Distribution5 versions - Latest release: 3 months ago - 9.27 thousand downloads total - 5 stars on GitHub - 1 maintainer
EpiCompare 1.12.0
Comparison, Benchmarking & QC of Epigenomic Datasets13 versions - Latest release: 3 months ago - 4.63 thousand downloads total - 17 stars on GitHub - 1 maintainer
mariner 1.8.1
Mariner: Explore the Hi-Cs6 versions - Latest release: 2 months ago - 4.49 thousand downloads total - 1 maintainer
roastgsa 1.6.0
Rotation based gene set analysis4 versions - Latest release: 3 months ago - 3.81 thousand downloads total - 0 stars on GitHub - 1 maintainer
plotgardener 1.14.0
Coordinate-Based Genomic Visualization Package for R10 versions - Latest release: 3 months ago - 4 dependent packages - 16.2 thousand downloads total - 320 stars on GitHub - 2 maintainers
EWCE 1.16.0
Expression Weighted Celltype Enrichment6 versions - Latest release: 2 months ago - 15.6 thousand downloads total - 53 stars on GitHub - 1 maintainer
pathwayPCA 1.24.0
Integrative Pathway Analysis with Modern PCA Methodology and Gene Selection5 versions - Latest release: 3 months ago - 1 dependent package - 11.6 thousand downloads total - 11 stars on GitHub - 1 maintainer
coMET 1.40.0
coMET: visualisation of regional epigenome-wide association scan (EWAS) results and DNA co-methyl...6 versions - Latest release: 3 months ago - 23.5 thousand downloads total - 1 maintainer
Related Keywords
Software
106
Sequencing
36
GeneExpression
35
RNASeq
30
Transcription
28
Epigenetics
28
Visualization
25
GeneRegulation
25
SystemsBiology
25
DifferentialExpression
24
Transcriptomics
23
GeneSetEnrichment
21
ImmunoOncology
20
Regression
19
Genetics
19
MultipleComparison
18
BiomedicalInformatics
18
DataImport
17
ChIPSeq
17
Clustering
15
QualityControl
15
FunctionalPrediction
14
Normalization
14
Preprocessing
14
Annotation
13
Coverage
13
CellBiology
12
AlternativeSplicing
12
Pathways
11
CRISPR
11
SNP
10
Classification
10
GenomeAnnotation
10
bioconductor
10
GeneTarget
10
BatchEffect
10
Network
10
bioconductor-package
9
SingleCell
9
Microarray
9
Proteomics
9
GenomicVariation
8
crispr
8
crispr-design
8
ATACSeq
7
grna
7
GenePrediction
7
Alignment
7
grna-sequence
7
DNAMethylation
7
grna-sequences
7
genomics
7
HiC
6
NetworkEnrichment
6
DifferentialSplicing
6
Bayesian
6
HistoneModification
6
PeakDetection
6
ComparativeGenomics
6
DifferentialMethylation
6
crispr-target
6
MethylSeq
6
GenomeWideAssociation
5
GO
5
GraphAndNetwork
5
crispr-analysis
5
rstats
5
VariantAnnotation
5
crispr-cas9
5
sgrna
5
sgrna-design
5
DataRepresentation
5
r
5
FeatureExtraction
5
WholeGenome
4
TimeCourse
4
PrincipalComponent
4
GeneticVariability
4
NetworkInference
4
TranscriptomeVariant
4
Survival
4
bioinformatics
4
MathematicalBiology
4
r-package
4
DNaseSeq
4
ReportWriting
3
Pharmacogenetics
3
DNA3DStructure
3
Phylogenetics
3
WorkflowStep
3
Pharmacogenomics
3
comparative-genomics
3
MethylationArray
3
Metabolomics
3
DifferentialPeakCalling
3
OneChannel
3
SequenceMatching
3
ProprietaryPlatforms
3
ThirdPartyClient
3
DimensionReduction
3