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
contiBAIT 1.30.0
Improves Early Build Genome Assemblies using Strand-Seq Data3 versions - Latest release: 6 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: 6 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: 6 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: 6 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: 6 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: 6 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: 6 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: 6 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: 6 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: 6 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: 6 months ago - 7.86 thousand downloads total - 1 maintainer
supersigs 1.10.0
Supervised mutational signatures3 versions - Latest release: 6 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: 6 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: 6 months ago - 12.2 thousand downloads total - 2 maintainers
globalSeq 1.30.0
Global Test for Counts3 versions - Latest release: 6 months ago - 10.4 thousand downloads total - 1 stars on GitHub - 1 maintainer
MEAL 1.32.0
Perform methylation analysis3 versions - Latest release: 6 months ago - 14.4 thousand downloads total - 1 maintainer
TVTB 1.28.0
TVTB: The VCF Tool Box3 versions - Latest release: 6 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: 6 months ago - 4.8 thousand downloads total - 1 maintainer
sscu 2.32.0
Strength of Selected Codon Usage3 versions - Latest release: 6 months ago - 9.78 thousand downloads total - 1 maintainer
mbQTL 1.2.0
mbQTL: A package for SNP-Taxa mGWAS analysis3 versions - Latest release: 6 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: 6 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: 6 months ago - 26.9 thousand downloads total - 1 maintainer
GeneBreak 1.32.0
Gene Break Detection3 versions - Latest release: 6 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: 6 months ago - 10.2 thousand downloads total - 1 maintainer
DMRScan 1.24.0
Detection of Differentially Methylated Regions3 versions - Latest release: 6 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: 6 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: 10 days ago - 991 downloads total - 6 stars on GitHub - 1 maintainer
Top 3.3% on bioconductor.org
4 versions - Latest release: 14 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: 14 days ago - 2 dependent packages - 135 thousand downloads total - 1 maintainer
Top 2.8% on bioconductor.org
3 versions - Latest release: 14 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: 14 days ago - 7 dependent packages - 208 thousand downloads total - 1 maintainer
doubletrouble 1.4.0
Identification and classification of duplicated genes6 versions - Latest release: 15 days ago - 1.65 thousand downloads total - 7 stars on GitHub - 1 maintainer
Top 5.7% on bioconductor.org
3 versions - Latest release: 21 days 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: 21 days 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: 19 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: 19 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: 21 days ago - 23 thousand downloads total - 64 stars on GitHub - 1 maintainer
compSPOT 1.0.0
compSPOT: Tool for identifying and comparing significantly mutated genomic hotspots1 version - Latest release: 7 months ago - 563 downloads total - 0 stars on GitHub - 1 maintainer
RAIDS 1.0.0
Accurate Inference of Genetic Ancestry from Cancer Sequences1 version - Latest release: 7 months ago - 708 downloads total - 5 stars on GitHub - 1 maintainer
methylCC 1.16.0
Estimate the cell composition of whole blood in DNA methylation samples2 versions - Latest release: 6 months ago - 6.03 thousand downloads total - 20 stars on GitHub - 1 maintainer
AneuFinder 1.30.0
Analysis of Copy Number Variation in Single-Cell-Sequencing Data2 versions - Latest release: 6 months ago - 17 thousand downloads total - 15 stars on GitHub - 1 maintainer
MethCP 1.13.0 removed
Differential methylation anlsysis for bisulfite sequencing data1 version - Latest release: 7 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: 7 months ago - 3.87 thousand downloads total - 1 maintainer
Related Keywords
Software
41
Sequencing
29
Genetics
12
ImmunoOncology
10
CopyNumberVariation
8
DNASeq
8
Coverage
7
DataImport
7
DNAMethylation
6
GenomicVariation
6
StatisticalMethod
6
ExomeSeq
5
Visualization
5
MultipleComparison
5
Classification
5
Alignment
5
DifferentialMethylation
5
Regression
4
SNP
4
Epigenetics
4
QualityControl
4
bioinformatics
4
Microarray
4
ComparativeGenomics
4
FunctionalGenomics
4
r
4
GeneExpression
4
Technology
3
VariantAnnotation
3
SomaticMutation
3
GenomeWideAssociation
3
MethylSeq
3
HiddenMarkovModel
3
SingleCell
3
DimensionReduction
2
BiologicalQuestion
2
DifferentialExpression
2
inheritance
2
TimeCourse
2
SequenceMatching
2
MultipleSequenceAlignment
2
genomics
2
GeneticVariability
2
r-package
2
Normalization
2
Preprocessing
2
rstats
2
Microbiome
2
Phylogenetics
2
whole-genome-sequencing
2
Network
2
GenomeAnnotation
2
cancer-genomics
2
comparative-genomics
2
MethylationArray
2
gene-duplication
1
swgs
1
monte-carlo-sampling
1
qPCR
1
GenePrediction
1
OneChannel
1
Clustering
1
TwoChannel
1
rna-sequencing
1
rna-seq
1
r-language
1
inference
1
exome-sequencing
1
ancestry
1
PrincipalComponent
1
Survival
1
vcf-files
1
summary-statistics
1
standardisation
1
qtl
1
gwas
1
database-api
1
bioconductor-package
1
genome-algebra
1
genome
1
genetic-code-algebra
1
genetic-code
1
MathematicalBiology
1
Pathways
1
GeneSetEnrichment
1
GO
1
whole-genome-duplication
1
molecular-evolution
1
differentially-methylated-elements
1
cpg
1
bioconductor
1
analysis
1
tumor-heterogeneity
1
hmm
1
genome-sequencing
1
copy-number-variation
1
10x-genomics
1
synteny-network
1
synteny
1
phylogenomics
1