Ecosyste.ms: Packages
An open API service providing package, version and dependency metadata of many open source software ecosystems and registries.
bioconductor.org "DNASeq" keyword
SARC 1.0.0
Statistical Analysis of Regions with CNVs2 versions - Latest release: 7 months ago - 933 downloads total - 0 stars on GitHub - 1 maintainer
Top 1.5% on bioconductor.org
3 versions - Latest release: about 1 month ago - 9 dependent packages - 227 thousand downloads total - 423 stars on GitHub - 1 maintainer
maftools 2.20.0 💰
Summarize, Analyze and Visualize MAF Files3 versions - Latest release: about 1 month ago - 9 dependent packages - 227 thousand downloads total - 423 stars on GitHub - 1 maintainer
compSPOT 1.0.0
compSPOT: Tool for identifying and comparing significantly mutated genomic hotspots2 versions - Latest release: 7 months ago - 899 downloads total - 0 stars on GitHub - 1 maintainer
miaSim 1.8.0
Microbiome Data Simulation3 versions - Latest release: 6 months ago - 3.45 thousand downloads total - 15 stars on GitHub - 1 maintainer
SigsPack 1.16.0
Mutational Signature Estimation for Single Samples3 versions - Latest release: 6 months ago - 5.08 thousand downloads total - 2 stars on GitHub - 1 maintainer
Clomial 1.38.0
Infers clonal composition of a tumor3 versions - Latest release: 7 months ago - 16.4 thousand downloads total - 1 maintainer
QSutils 1.20.0
Quasispecies Diversity3 versions - Latest release: 7 months ago - 19.7 thousand downloads total - 1 maintainer
Top 7.1% on bioconductor.org
3 versions - Latest release: 7 months ago - 22.4 thousand downloads total - 87 stars on GitHub - 1 maintainer
TitanCNA 1.40.0
Subclonal copy number and LOH prediction from whole genome sequencing of tumours3 versions - Latest release: 7 months ago - 22.4 thousand downloads total - 87 stars on GitHub - 1 maintainer
Top 2.9% on bioconductor.org
3 versions - Latest release: 29 days ago - 8 dependent packages - 85.8 thousand downloads total - 287 stars on GitHub - 1 maintainer
karyoploteR 1.30.0
Plot customizable linear genomes displaying arbitrary data3 versions - Latest release: 29 days ago - 8 dependent packages - 85.8 thousand downloads total - 287 stars on GitHub - 1 maintainer
SPsimSeq 1.12.0
Semi-parametric simulation tool for bulk and single-cell RNA sequencing data3 versions - Latest release: 6 months ago - 2 dependent packages - 5.36 thousand downloads total - 10 stars on GitHub - 1 maintainer
uSORT 1.28.0
uSORT: A self-refining ordering pipeline for gene selection3 versions - Latest release: 7 months ago - 9.91 thousand downloads total - 1 maintainer
seq.hotSPOT 1.2.0
Targeted sequencing panel design based on mutation hotspots3 versions - Latest release: 7 months ago - 1.08 thousand downloads total - 0 stars on GitHub - 1 maintainer
omicplotR 1.22.0
Visual Exploration of Omic Datasets Using a Shiny App3 versions - Latest release: 7 months ago - 8.13 thousand downloads total - 1 maintainer
HGC 1.10.0
A fast hierarchical graph-based clustering method3 versions - Latest release: 7 months ago - 3.61 thousand downloads total - 1 maintainer
tweeDEseq 1.48.0
RNA-seq data analysis using the Poisson-Tweedie family of distributions3 versions - Latest release: 7 months ago - 32.2 thousand downloads total - 0 stars on GitHub - 1 maintainer
CNVfilteR 1.16.0
Identifies false positives of CNV calling tools by using SNV calls3 versions - Latest release: 7 months ago - 5.74 thousand downloads total - 3 stars on GitHub - 1 maintainer
esATAC 1.24.0
An Easy-to-use Systematic pipeline for ATACseq data analysis3 versions - Latest release: 7 months ago - 20.2 thousand downloads total - 22 stars on GitHub - 1 maintainer
MMAPPR2 1.16.0
Mutation Mapping Analysis Pipeline for Pooled RNA-Seq3 versions - Latest release: 7 months ago - 3.34 thousand downloads total - 1 maintainer
RcwlPipelines 1.18.1
Bioinformatics pipelines based on Rcwl4 versions - Latest release: about 1 month ago - 1 dependent package - 8 thousand downloads total - 1 maintainer
decompTumor2Sig 2.18.0
Decomposition of individual tumors into mutational signatures by signature refitting3 versions - Latest release: 7 months ago - 1 dependent package - 8.89 thousand downloads total - 1 maintainer
regioneReloaded 1.4.0
RegioneReloaded: Multiple Association for Genomic Region Sets3 versions - Latest release: 7 months ago - 1.61 thousand downloads total - 5 stars on GitHub - 1 maintainer
CopyNumberPlots 1.18.0
Create Copy-Number Plots using karyoploteR functionality3 versions - Latest release: 7 months ago - 2 dependent packages - 9.48 thousand downloads total - 6 stars on GitHub - 1 maintainer
TVTB 1.28.0
TVTB: The VCF Tool Box3 versions - Latest release: 7 months ago - 9.85 thousand downloads total - 2 stars on GitHub - 1 maintainer
SCOPE 1.14.0
A normalization and copy number estimation method for single-cell DNA sequencing3 versions - Latest release: 7 months ago - 4.8 thousand downloads total - 1 maintainer
NADfinder 1.26.0
Call wide peaks for sequencing data3 versions - Latest release: 7 months ago - 9.86 thousand downloads total - 2 maintainers
YAPSA 1.28.0
Yet Another Package for Signature Analysis3 versions - Latest release: 7 months ago - 16.5 thousand downloads total - 1 maintainer
dearseq 1.14.0
Differential Expression Analysis for RNA-seq data through a robust variance component test3 versions - Latest release: 7 months ago - 2 dependent packages - 8.25 thousand downloads total - 6 stars on GitHub - 1 maintainer
CNAnorm 1.48.0
A normalization method for Copy Number Aberration in cancer samples3 versions - Latest release: 7 months ago - 26.9 thousand downloads total - 1 maintainer
semisup 1.26.0
Semi-Supervised Mixture Model3 versions - Latest release: 7 months ago - 7.99 thousand downloads total - 1 stars on GitHub - 1 maintainer
ATACseqQC 1.26.0
ATAC-seq Quality Control3 versions - Latest release: 7 months ago - 2 dependent packages - 42.4 thousand downloads total - 1 maintainer
GeneBreak 1.32.0
Gene Break Detection3 versions - Latest release: 7 months ago - 11.9 thousand downloads total - 2 stars on GitHub - 1 maintainer
CNViz 1.10.0
Copy Number Visualization3 versions - Latest release: 7 months ago - 2.93 thousand downloads total - 1 maintainer
coMET 1.34.0
coMET: visualisation of regional epigenome-wide association scan (EWAS) results and DNA co-methyl...3 versions - Latest release: 7 months ago - 21.1 thousand downloads total - 1 maintainer
spatialHeatmap 2.10.0
spatialHeatmap8 versions - Latest release: 18 days ago - 5.78 thousand downloads total - 4 stars on GitHub - 1 maintainer
Top 2.2% on bioconductor.org
3 versions - Latest release: 24 days ago - 13 dependent packages - 217 thousand downloads total - 1 maintainer
regioneR 1.36.0
Association analysis of genomic regions based on permutation tests3 versions - Latest release: 24 days ago - 13 dependent packages - 217 thousand downloads total - 1 maintainer
Top 4.0% on bioconductor.org
3 versions - Latest release: 24 days ago - 4 dependent packages - 75.9 thousand downloads total - 24 stars on GitHub - 1 maintainer
ALDEx2 1.36.0
Analysis Of Differential Abundance Taking Sample and Scale Variation Into Account3 versions - Latest release: 24 days ago - 4 dependent packages - 75.9 thousand downloads total - 24 stars on GitHub - 1 maintainer
Top 5.7% on bioconductor.org
3 versions - Latest release: 24 days ago - 50.3 thousand downloads total - 194 stars on GitHub - 1 maintainer
GenVisR 1.36.0
Genomic Visualizations in R3 versions - Latest release: 24 days ago - 50.3 thousand downloads total - 194 stars on GitHub - 1 maintainer
Top 5.4% on bioconductor.org
3 versions - Latest release: about 1 month ago - 4 dependent packages - 48.1 thousand downloads total - 43 stars on GitHub - 1 maintainer
QDNAseq 1.40.0
Quantitative DNA Sequencing for Chromosomal Aberrations3 versions - Latest release: about 1 month ago - 4 dependent packages - 48.1 thousand downloads total - 43 stars on GitHub - 1 maintainer
breakpointR 1.22.0
Find breakpoints in Strand-seq data3 versions - Latest release: 26 days ago - 7.39 thousand downloads total - 8 stars on GitHub - 1 maintainer
seqArchR 1.8.0
Identify Different Architectures of Sequence Elements3 versions - Latest release: 27 days ago - 1 dependent package - 2.62 thousand downloads total - 1 stars on GitHub - 1 maintainer
ATACseqTFEA 1.6.0
Transcription Factor Enrichment Analysis for ATAC-seq3 versions - Latest release: 27 days ago - 1.98 thousand downloads total - 0 stars on GitHub - 1 maintainer
ACE 1.22.0
Absolute Copy Number Estimation from Low-coverage Whole Genome Sequencing3 versions - Latest release: 29 days ago - 8.72 thousand downloads total - 11 stars on GitHub - 1 maintainer
nempi 1.12.0
Inferring unobserved perturbations from gene expression data3 versions - Latest release: about 1 month ago - 2.89 thousand downloads total - 2 stars on GitHub - 1 maintainer
mnem 1.20.0
Mixture Nested Effects Models3 versions - Latest release: about 1 month ago - 4 dependent packages - 8.23 thousand downloads total - 4 stars on GitHub - 1 maintainer
Related Keywords
Software
44
Sequencing
32
CopyNumberVariation
13
Visualization
13
Genetics
13
RNASeq
12
ImmunoOncology
10
Coverage
10
WholeGenome
8
SingleCell
8
ATACSeq
7
Clustering
7
DataImport
7
GeneExpression
7
GenomicVariation
6
ChIPSeq
5
SomaticMutation
5
MultipleComparison
5
Alignment
5
DifferentialExpression
5
Classification
5
QualityControl
5
DataRepresentation
4
Transcriptomics
4
GeneRegulation
4
SystemsBiology
4
MethylSeq
4
Network
4
StatisticalMethod
4
Microarray
3
bioconductor
3
CellBiology
3
GUI
3
Preprocessing
3
PooledScreens
3
r
3
GeneticVariability
3
ExomeSeq
3
Bayesian
3
SNP
3
bioinformatics
3
VariantAnnotation
3
BiomedicalInformatics
3
Microbiome
3
genomics
2
Metagenomics
2
GraphAndNetwork
2
Survival
2
BiologicalQuestion
2
r-package
2
Normalization
2
FunctionalGenomics
2
FeatureExtraction
2
DifferentialMethylation
2
CRISPR
2
NetworkInference
2
Pathways
2
rstats
2
SequenceMatching
2
OneChannel
2
genomics-visualization
2
Technology
2
copy-number-variation
2
MathematicalBiology
1
DimensionReduction
1
GenomeAnnotation
1
Infrastructure
1
Scale simulation
1
Posterior p-value
1
TissueMicroarray
1
Spatial
1
GeneTarget
1
CellBasedAssays
1
RiboSeq
1
MotifAnnotation
1
MethylationArray
1
MotifDiscovery
1
clustering
1
nmf
1
nonnegative-matrix-factorization
1
promoter-sequence-architectures
1
scikit-learn
1
sequence-analysis
1
sequence-architectures
1
unsupervised-machine-learning
1
MNaseSeq
1
HiddenMarkovModel
1
GeneSignaling
1
NeuralNetwork
1
TargetedResequencing
1
tcga
1
maf-files
1
cancer-genomics
1
plotting-in-r
1
cancer-genome-atlas
1
DNaseSeq
1
genome
1
data-visualization
1
atac-seq
1
pipeline
1