bioconductor.org "DNASeq" keyword
HGC 1.20.0
A fast hierarchical graph-based clustering method7 versions - Latest release: 6 months ago - 19.7 thousand downloads total - 1 maintainer
CNAnorm 1.58.0
A normalization method for Copy Number Aberration in cancer samples7 versions - Latest release: 5 months ago - 48 thousand downloads total - 1 maintainer
ATACseqQC 1.36.1
ATAC-seq Quality Control8 versions - Latest release: 3 months ago - 2 dependent packages - 84.7 thousand downloads total - 1 maintainer
Top 2.2% on bioconductor.org
8 versions - Latest release: 5 months ago - 13 dependent packages - 371 thousand downloads total - 1 maintainer
regioneR 1.44.0
Association analysis of genomic regions based on permutation tests8 versions - Latest release: 5 months ago - 13 dependent packages - 371 thousand downloads total - 1 maintainer
Top 2.9% on bioconductor.org
8 versions - Latest release: 6 months ago - 8 dependent packages - 173 thousand downloads total - 377 stars on GitHub - 1 maintainer
karyoploteR 1.38.0
Plot customizable linear genomes displaying arbitrary data8 versions - Latest release: 6 months ago - 8 dependent packages - 173 thousand downloads total - 377 stars on GitHub - 1 maintainer
RcwlPipelines 1.28.0
Bioinformatics pipelines based on Rcwl8 versions - Latest release: 5 months ago - 1 dependent package - 24.2 thousand downloads total - 1 maintainer
fRagmentomics 1.0.0
Extract Fragmentomics Features and Mutational Status1 version - Latest release: 6 months ago - 8.35 thousand downloads total - 13 stars on GitHub - 1 maintainer
QSutils 1.30.0
Quasispecies Diversity7 versions - Latest release: 6 months ago - 42.2 thousand downloads total - 1 maintainer
Top 5.7% on bioconductor.org
8 versions - Latest release: 5 months ago - 85.8 thousand downloads total - 194 stars on GitHub - 1 maintainer
GenVisR 1.44.0
Genomic Visualizations in R8 versions - Latest release: 5 months ago - 85.8 thousand downloads total - 194 stars on GitHub - 1 maintainer
Top 1.5% on bioconductor.org
7 versions - Latest release: 6 months ago - 9 dependent packages - 381 thousand downloads total - 505 stars on GitHub - 1 maintainer
maftools 2.28.0 💰
Summarize, Analyze and Visualize MAF Files7 versions - Latest release: 6 months ago - 9 dependent packages - 381 thousand downloads total - 505 stars on GitHub - 1 maintainer
SCOPE 1.24.0
A normalization and copy number estimation method for single-cell DNA sequencing7 versions - Latest release: 5 months ago - 1 maintainer
fraq 1.0.2
A High-Throughput and Extensible Toolkit for Processing FASTQ Data2 versions - Latest release: 2 months ago - 5.79 thousand downloads total - 1 stars on GitHub - 1 maintainer
miaSim 1.18.0
Microbiome Data Simulation7 versions - Latest release: 5 months ago - 22 stars on GitHub - 1 maintainer
NADfinder 1.36.0
Call wide peaks for sequencing data7 versions - Latest release: 6 months ago - 34.1 thousand downloads total - 2 maintainers
GeneBreak 1.42.0
Gene Break Detection7 versions - Latest release: 5 months ago - 34 thousand downloads total - 2 stars on GitHub - 1 maintainer
CopyNumberPlots 1.28.0
Create Copy-Number Plots using karyoploteR functionality8 versions - Latest release: 5 months ago - 2 dependent packages - 29.3 thousand downloads total - 7 stars on GitHub - 1 maintainer
spatialHeatmap 2.18.2
spatialHeatmap: Visualizing Spatial Assays in Anatomical Images and Large-Scale Data Extensions18 versions - Latest release: 4 months ago - 23.4 thousand downloads total - 6 stars on GitHub - 1 maintainer
uSORT 1.38.0
uSORT: A self-refining ordering pipeline for gene selection7 versions - Latest release: 5 months ago - 29.5 thousand downloads total - 1 maintainer
mnem 1.28.0
Mixture Nested Effects Models7 versions - Latest release: 5 months ago - 4 dependent packages - 22.7 thousand downloads total - 4 stars on GitHub - 1 maintainer
compSPOT 1.10.0
compSPOT: Tool for identifying and comparing significantly mutated genomic hotspots6 versions - Latest release: 6 months ago - 8.81 thousand downloads total - 0 stars on GitHub - 1 maintainer
seq.hotSPOT 1.12.0
Targeted sequencing panel design based on mutation hotspots7 versions - Latest release: 6 months ago - 10 thousand downloads total - 0 stars on GitHub - 1 maintainer
omicplotR 1.32.0
Visual Exploration of Omic Datasets Using a Shiny App7 versions - Latest release: 5 months ago - 20.2 thousand downloads total - 1 maintainer
regioneReloaded 1.14.0
RegioneReloaded: Multiple Association for Genomic Region Sets7 versions - Latest release: 6 months ago - 11.1 thousand downloads total - 5 stars on GitHub - 1 maintainer
decompTumor2Sig 2.28.1
Decomposition of individual tumors into mutational signatures by signature refitting8 versions - Latest release: 3 months ago - 1 dependent package - 23.8 thousand downloads total - 1 maintainer
Clomial 1.48.0
Infers clonal composition of a tumor7 versions - Latest release: 6 months ago - 29.2 thousand downloads total - 1 maintainer
breakpointR 1.30.0
Find breakpoints in Strand-seq data7 versions - Latest release: 5 months ago - 22.2 thousand downloads total - 9 stars on GitHub - 1 maintainer
TVTB 1.38.0
TVTB: The VCF Tool Box9 versions - Latest release: 6 months ago - 23.3 thousand downloads total - 2 stars on GitHub - 1 maintainer
Top 5.4% on bioconductor.org
7 versions - Latest release: 6 months ago - 4 dependent packages - 93.5 thousand downloads total - 57 stars on GitHub - 1 maintainer
QDNAseq 1.48.0
Quantitative DNA Sequencing for Chromosomal Aberrations7 versions - Latest release: 6 months ago - 4 dependent packages - 93.5 thousand downloads total - 57 stars on GitHub - 1 maintainer
tweeDEseq 1.58.0
RNA-seq data analysis using the Poisson-Tweedie family of distributions7 versions - Latest release: 5 months ago - 48.7 thousand downloads total - 1 stars on GitHub - 1 maintainer
ATACseqTFEA 1.14.0
Transcription Factor Enrichment Analysis for ATAC-seq7 versions - Latest release: 6 months ago - 13.7 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 4.0% on bioconductor.org
7 versions - Latest release: 6 months ago - 4 dependent packages - 165 thousand downloads total - 31 stars on GitHub - 1 maintainer
ALDEx2 1.44.0
Analysis Of Differential Abundance Taking Sample and Scale Variation Into Account7 versions - Latest release: 6 months ago - 4 dependent packages - 165 thousand downloads total - 31 stars on GitHub - 1 maintainer
CNVfilteR 1.26.0
Identifies false positives of CNV calling tools by using SNV calls8 versions - Latest release: 5 months ago - 17.5 thousand downloads total - 6 stars on GitHub - 1 maintainer
SigsPack 1.26.0
Mutational Signature Estimation for Single Samples7 versions - Latest release: 6 months ago - 17.6 thousand downloads total - 2 stars on GitHub - 1 maintainer
dearseq 1.24.0
Differential Expression Analysis for RNA-seq data through a robust variance component test7 versions - Latest release: 5 months ago - 2 dependent packages - 26.7 thousand downloads total - 6 stars on GitHub - 1 maintainer
ACE 1.30.0
Absolute Copy Number Estimation from Low-coverage Whole Genome Sequencing7 versions - Latest release: 4 months ago - 24.2 thousand downloads total - 21 stars on GitHub - 1 maintainer
SPsimSeq 1.22.0
Semi-parametric simulation tool for bulk and single-cell RNA sequencing data7 versions - Latest release: 6 months ago - 2 dependent packages - 18.6 thousand downloads total - 10 stars on GitHub - 1 maintainer
semisup 1.36.0
Semi-Supervised Mixture Model7 versions - Latest release: 6 months ago - 18.9 thousand downloads total - 1 stars on GitHub - 1 maintainer
nempi 1.20.0
Inferring unobserved perturbations from gene expression data7 versions - Latest release: 6 months ago - 13.3 thousand downloads total - 2 stars on GitHub - 1 maintainer
YAPSA 1.38.0
Yet Another Package for Signature Analysis8 versions - Latest release: 6 months ago - 44 thousand downloads total - 1 maintainer
CNViz 1.20.0
Copy Number Visualization7 versions - Latest release: 6 months ago - 16.1 thousand downloads total - 1 maintainer
Top 7.1% on bioconductor.org
6 versions - Latest release: 11 months ago - 30 thousand downloads total - 103 stars on GitHub - 1 maintainer
TitanCNA 1.48.0 removed
Subclonal copy number and LOH prediction from whole genome sequencing of tumours6 versions - Latest release: 11 months ago - 30 thousand downloads total - 103 stars on GitHub - 1 maintainer
esATAC 1.34.0
An Easy-to-use Systematic pipeline for ATACseq data analysis7 versions - Latest release: 5 months ago - 42.9 thousand downloads total - 24 stars on GitHub - 1 maintainer
seqArchR 1.14.0 removed
Identify Different Architectures of Sequence Elements6 versions - Latest release: 11 months ago - 1 dependent package - 8.2 thousand downloads total - 2 stars on GitHub - 1 maintainer
SARC 1.7.1 removed
Statistical Analysis of Regions with CNVs5 versions - Latest release: 11 months ago - 5.26 thousand downloads total - 0 stars on GitHub - 1 maintainer
coMET 1.40.0 removed
coMET: visualisation of regional epigenome-wide association scan (EWAS) results and DNA co-methyl...6 versions - Latest release: over 1 year ago - 24.4 thousand downloads total - 1 maintainer
MMAPPR2 1.18.0 removed
Mutation Mapping Analysis Pipeline for Pooled RNA-Seq3 versions - Latest release: over 2 years ago - 3.62 thousand downloads total - 1 maintainer
Related Keywords
Software
46
Sequencing
34
Genetics
14
CopyNumberVariation
13
Visualization
13
RNASeq
12
Coverage
10
ImmunoOncology
10
WholeGenome
8
SingleCell
8
DataImport
7
Alignment
7
GeneExpression
7
Clustering
7
ATACSeq
7
GenomicVariation
6
QualityControl
6
DifferentialExpression
5
ChIPSeq
5
MultipleComparison
5
Classification
5
SomaticMutation
5
GeneRegulation
4
SystemsBiology
4
StatisticalMethod
4
Transcriptomics
4
Network
4
DataRepresentation
4
MethylSeq
4
SNP
3
BiomedicalInformatics
3
PooledScreens
3
Microbiome
3
GUI
3
GeneticVariability
3
r
3
bioinformatics
3
Bayesian
3
bioconductor
3
VariantAnnotation
3
CellBiology
3
ExomeSeq
3
Microarray
3
Preprocessing
3
BiologicalQuestion
2
VariantDetection
2
CRISPR
2
NetworkInference
2
GraphAndNetwork
2
Pathways
2
SequenceMatching
2
DifferentialMethylation
2
FunctionalGenomics
2
copy-number-variation
2
Normalization
2
OneChannel
2
FeatureExtraction
2
Metagenomics
2
Infrastructure
2
Technology
2
genomics
2
rstats
2
r-package
2
Survival
2
genomics-visualization
2
NucleosomePositioning
1
atac-seq
1
MotifDiscovery
1
TimeCourse
1
pipeline
1
GeneSignaling
1
Transcription
1
NeuralNetwork
1
WorkflowStep
1
DNaseSeq
1
tcga
1
maf-files
1
DNAMethylation
1
GenomeWideAssociation
1
MethylationArray
1
cancer-genomics
1
cancer-genome-atlas
1
MotifAnnotation
1
RiboSeq
1
Posterior p-value
1
Scale simulation
1
DriverMutation
1
MathematicalBiology
1
DimensionReduction
1
aCGH
1
MNaseSeq
1
bioconductor-package
1
PeakDetection
1
GenomeAnnotation
1
TissueMicroarray
1
Spatial
1
GeneTarget
1
CellBasedAssays
1
tumor-heterogeneity
1
hmm
1