Ecosyste.ms: Packages
An open API service providing package, version and dependency metadata of many open source software ecosystems and registries.
bioconductor.org "WholeGenome" keyword
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
RAIDS 1.0.0
Accurate Inference of Genetic Ancestry from Cancer Sequences2 versions - Latest release: 7 months ago - 1.03 thousand downloads total - 5 stars on GitHub - 1 maintainer
methylCC 1.16.0
Estimate the cell composition of whole blood in DNA methylation samples3 versions - Latest release: 6 months ago - 6.38 thousand downloads total - 20 stars on GitHub - 1 maintainer
AneuFinder 1.30.0
Analysis of Copy Number Variation in Single-Cell-Sequencing Data3 versions - Latest release: 6 months ago - 17.5 thousand downloads total - 15 stars on GitHub - 1 maintainer
contiBAIT 1.30.0
Improves Early Build Genome Assemblies using Strand-Seq Data3 versions - Latest release: 7 months ago - 10.7 thousand downloads total - 1 maintainer
syntenet 1.4.2
Inference And Analysis Of Synteny Networks4 versions - Latest release: about 1 month ago - 1 dependent package - 3.4 thousand downloads total - 14 stars on GitHub - 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
iCNV 1.22.0
Integrated Copy Number Variation detection3 versions - Latest release: 7 months ago - 7.74 thousand downloads total - 1 maintainer
katdetectr 1.4.0
Detection, Characterization and Visualization of Kataegis in Sequencing Data3 versions - Latest release: 7 months ago - 1.91 thousand downloads total - 1 maintainer
BadRegionFinder 1.30.0
BadRegionFinder: an R/Bioconductor package for identifying regions with bad coverage3 versions - Latest release: 7 months ago - 11.5 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
dmrseq 1.22.1
Detection and inference of differentially methylated regions from Whole Genome Bisulfite Sequencing4 versions - Latest release: 2 months ago - 1 dependent package - 17.9 thousand downloads total - 1 maintainer
methylInheritance 1.26.0
Permutation-Based Analysis associating Conserved Differentially Methylated Elements Across Multip...3 versions - Latest release: 7 months ago - 1 dependent package - 9.5 thousand downloads total - 0 stars on GitHub - 1 maintainer
podkat 1.34.0
Position-Dependent Kernel Association Test3 versions - Latest release: 7 months ago - 13.8 thousand downloads total - 0 stars on GitHub - 1 maintainer
Summix 2.8.0
Summix2: A suite of methods to estimate, adjust, and leverage substructure in genetic summary data3 versions - Latest release: 7 months ago - 2.59 thousand downloads total - 1 maintainer
RVS 1.24.0
Computes estimates of the probability of related individuals sharing a rare variant3 versions - Latest release: 7 months ago - 7.86 thousand downloads total - 1 maintainer
supersigs 1.10.0
Supervised mutational signatures3 versions - Latest release: 7 months ago - 2.71 thousand downloads total - 3 stars on GitHub - 1 maintainer
methInheritSim 1.24.0
Simulating Whole-Genome Inherited Bisulphite Sequencing Data3 versions - Latest release: 7 months ago - 1 dependent package - 8.46 thousand downloads total - 1 stars on GitHub - 1 maintainer
LowMACA 1.31.0 removed
LowMACA - Low frequency Mutation Analysis via Consensus Alignment2 versions - Latest release: 7 months ago - 12.2 thousand downloads total - 2 maintainers
globalSeq 1.30.0
Global Test for Counts3 versions - Latest release: 7 months ago - 10.4 thousand downloads total - 1 stars on GitHub - 1 maintainer
MEAL 1.32.0
Perform methylation analysis3 versions - Latest release: 7 months ago - 14.4 thousand downloads total - 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
sscu 2.32.0
Strength of Selected Codon Usage3 versions - Latest release: 7 months ago - 9.78 thousand downloads total - 1 maintainer
mbQTL 1.2.0
mbQTL: A package for SNP-Taxa mGWAS analysis3 versions - Latest release: 7 months ago - 1.26 thousand downloads total - 1 maintainer
RareVariantVis 2.30.0
A suite for analysis of rare genomic variants in whole genome sequencing data3 versions - Latest release: 7 months ago - 12.1 thousand downloads total - 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
GeneBreak 1.32.0
Gene Break Detection3 versions - Latest release: 7 months ago - 11.9 thousand downloads total - 2 stars on GitHub - 1 maintainer
Uniquorn 2.22.0
Identification of cancer cell lines based on their weighted mutational/ variational fingerprint3 versions - Latest release: 7 months ago - 10.2 thousand downloads total - 1 maintainer
DMRScan 1.24.0
Detection of Differentially Methylated Regions3 versions - Latest release: 7 months ago - 8.77 thousand downloads total - 2 stars on GitHub - 1 maintainer
cfDNAPro 1.8.0
cfDNAPro extracts and Visualises biological features from whole genome sequencing data of cell-fr...3 versions - Latest release: 7 months ago - 3.41 thousand downloads total - 22 stars on GitHub - 1 maintainer
cfdnakit 1.2.0
Fragmen-length analysis package from high-throughput sequencing of cell-free DNA (cfDNA)3 versions - Latest release: 19 days ago - 991 downloads total - 6 stars on GitHub - 1 maintainer
Top 3.3% on bioconductor.org
4 versions - Latest release: 23 days ago - 2 dependent packages - 135 thousand downloads total - 1 maintainer
DMRcate 3.0.0
Methylation array and sequencing spatial analysis methods4 versions - Latest release: 23 days ago - 2 dependent packages - 135 thousand downloads total - 1 maintainer
Top 2.8% on bioconductor.org
3 versions - Latest release: 24 days ago - 7 dependent packages - 208 thousand downloads total - 1 maintainer
DECIPHER 3.0.0
Tools for curating, analyzing, and manipulating biological sequences3 versions - Latest release: 24 days ago - 7 dependent packages - 208 thousand downloads total - 1 maintainer
doubletrouble 1.4.0
Identification and classification of duplicated genes6 versions - Latest release: 25 days ago - 1.65 thousand downloads total - 7 stars on GitHub - 1 maintainer
Top 5.7% on bioconductor.org
3 versions - Latest release: about 1 month ago - 3 dependent packages - 47.1 thousand downloads total - 76 stars on GitHub - 1 maintainer
rGREAT 2.6.0
GREAT Analysis - Functional Enrichment on Genomic Regions3 versions - Latest release: about 1 month ago - 3 dependent packages - 47.1 thousand downloads total - 76 stars on GitHub - 1 maintainer
GenomAutomorphism 1.6.0
Compute the automorphisms between DNA's Abelian group representations3 versions - Latest release: 28 days ago - 1.4 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
MungeSumstats 1.12.0
Standardise summary statistics from GWAS4 versions - Latest release: about 1 month ago - 23 thousand downloads total - 64 stars on GitHub - 1 maintainer
MethCP 1.13.0 removed
Differential methylation anlsysis for bisulfite sequencing data1 version - Latest release: 8 months ago - 2.97 thousand downloads total - 4 stars on GitHub - 1 maintainer
PrecisionTrialDrawer 1.16.0 removed
A Tool to Analyze and Design NGS Based Custom Gene Panels1 version - Latest release: 8 months ago - 3.87 thousand downloads total - 1 maintainer
Related Keywords
Software
41
Sequencing
29
Genetics
12
ImmunoOncology
10
DNASeq
8
CopyNumberVariation
8
Coverage
7
DataImport
7
StatisticalMethod
6
GenomicVariation
6
DNAMethylation
6
ExomeSeq
5
Alignment
5
DifferentialMethylation
5
Classification
5
MultipleComparison
5
Visualization
5
Epigenetics
4
FunctionalGenomics
4
ComparativeGenomics
4
QualityControl
4
Regression
4
GeneExpression
4
Microarray
4
SNP
4
bioinformatics
4
r
4
VariantAnnotation
3
MethylSeq
3
SingleCell
3
HiddenMarkovModel
3
Technology
3
GenomeWideAssociation
3
SomaticMutation
3
TimeCourse
2
r-package
2
BiologicalQuestion
2
Normalization
2
DifferentialExpression
2
Preprocessing
2
SequenceMatching
2
GenomeAnnotation
2
inheritance
2
MultipleSequenceAlignment
2
Microbiome
2
whole-genome-sequencing
2
MethylationArray
2
genomics
2
Network
2
Phylogenetics
2
comparative-genomics
2
cancer-genomics
2
rstats
2
GeneticVariability
2
DimensionReduction
2
genomics-visualization
1
early-detection
1
database-api
1
DataRepresentation
1
gwas
1
GUI
1
cell-free-dna
1
cancer-research
1
vcf-files
1
aCGH
1
qtl
1
summary-statistics
1
Metagenomics
1
standardisation
1
molecular-evolution
1
gene-duplication
1
whole-genome-duplication
1
GO
1
qPCR
1
GenePrediction
1
Clustering
1
TwoChannel
1
GeneSetEnrichment
1
Pathways
1
MathematicalBiology
1
genetic-code
1
genetic-code-algebra
1
genome
1
OneChannel
1
genome-algebra
1
swgs
1
bioconductor-package
1
liquid-biopsy
1
miRNA
1
10x-genomics
1
synteny-network
1
synteny
1
phylogenomics
1
network-science
1
evolutionary-genomics
1
SystemsBiology
1
NetworkInference
1
GraphAndNetwork
1
GenomeAssembly
1
CellBasedAssays
1