Ecosyste.ms: Packages
An open API service providing package, version and dependency metadata of many open source software ecosystems and registries.
bioconductor.org "FeatureExtraction" keyword
Top 1.5% on bioconductor.org
3 versions - Latest release: 20 days ago - 9 dependent packages - 226 thousand downloads total - 421 stars on GitHub - 1 maintainer
maftools 2.20.0 💰
Summarize, Analyze and Visualize MAF Files3 versions - Latest release: 20 days ago - 9 dependent packages - 226 thousand downloads total - 421 stars on GitHub - 1 maintainer
quantiseqr 1.10.0
Quantification of the Tumor Immune contexture from RNA-seq data3 versions - Latest release: 6 months ago - 2 dependent packages - 11.8 thousand downloads total - 1 maintainer
FEAST 1.10.0
FEAture SelcTion (FEAST) for Single-cell clustering3 versions - Latest release: 6 months ago - 4.7 thousand downloads total - 9 stars on GitHub - 1 maintainer
mAPKL 1.32.0 removed
A Hybrid Feature Selection method for gene expression data2 versions - Latest release: 6 months ago - 11.8 thousand downloads total - 1 maintainer
rScudo 1.18.1
Signature-based Clustering for Diagnostic Purposes4 versions - Latest release: 3 months ago - 5.75 thousand downloads total - 3 stars on GitHub - 1 maintainer
HIREewas 1.20.0
Detection of cell-type-specific risk-CpG sites in epigenome-wide association studies3 versions - Latest release: 6 months ago - 5.89 thousand downloads total - 1 maintainer
GARS 1.22.0
GARS: Genetic Algorithm for the identification of Robust Subsets of variables in high-dimensional...3 versions - Latest release: 6 months ago - 8.17 thousand downloads total - 1 maintainer
FeatSeekR 1.2.0
FeatSeekR an R package for unsupervised feature selection3 versions - Latest release: 6 months ago - 1.19 thousand downloads total - 1 stars on GitHub - 1 maintainer
SIAMCAT 2.6.0
Statistical Inference of Associations between Microbial Communities And host phenoTypes3 versions - Latest release: 6 months ago - 11.8 thousand downloads total - 1 maintainer
sigFeature 1.20.0
sigFeature: Significant feature selection using SVM-RFE & t-statistic3 versions - Latest release: 6 months ago - 12.7 thousand downloads total - 1 maintainer
BPRMeth 1.28.0
Model higher-order methylation profiles3 versions - Latest release: 6 months ago - 1 dependent package - 11.9 thousand downloads total - 1 maintainer
scMET 1.4.0
Bayesian modelling of cell-to-cell DNA methylation heterogeneity3 versions - Latest release: 6 months ago - 1.73 thousand downloads total - 18 stars on GitHub - 1 maintainer
bambu 3.4.1
Context-Aware Transcript Quantification from Long Read RNA-Seq data4 versions - Latest release: about 1 month ago - 1 dependent package - 13 thousand downloads total - 118 stars on GitHub - 1 maintainer
Top 7.2% on bioconductor.org
3 versions - Latest release: 6 months ago - 1 dependent package - 33.5 thousand downloads total - 1 maintainer
Rcpi 1.38.0
Molecular Informatics Toolkit for Compound-Protein Interaction in Drug Discovery3 versions - Latest release: 6 months ago - 1 dependent package - 33.5 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
KnowSeq 1.16.0
KnowSeq R/Bioc package: The Smart Transcriptomic Pipeline3 versions - Latest release: 6 months ago - 6.15 thousand downloads total - 1 maintainer
BUMHMM 1.26.0
Computational pipeline for computing probability of modification from structure probing experimen...3 versions - Latest release: 6 months ago - 9.56 thousand downloads total - 1 maintainer
ORFhunteR 1.10.0
Predict open reading frames in nucleotide sequences3 versions - Latest release: 6 months ago - 3.05 thousand downloads total - 1 stars on GitHub - 1 maintainer
Melissa 1.18.0
Bayesian clustering and imputationa of single cell methylomes3 versions - Latest release: 6 months ago - 5.54 thousand downloads total - 1 maintainer
multiClust 1.32.0
multiClust: An R-package for Identifying Biologically Relevant Clusters in Cancer Transcriptome P...3 versions - Latest release: 6 months ago - 14.3 thousand downloads total - 1 maintainer
synlet 2.2.0
Hits Selection for Synthetic Lethal RNAi Screen Data3 versions - Latest release: 6 months ago - 10.8 thousand downloads total - 1 maintainer
DepecheR 1.18.0
Determination of essential phenotypic elements of clusters in high-dimensional entities3 versions - Latest release: 6 months ago - 1 dependent package - 16 thousand downloads total - 1 maintainer
TDbasedUFE 1.2.0
Tensor Decomposition Based Unsupervised Feature Extraction3 versions - Latest release: 6 months ago - 1 dependent package - 1.75 thousand downloads total - 5 stars on GitHub - 1 maintainer
zFPKM 1.24.0
A suite of functions to facilitate zFPKM transformations3 versions - Latest release: 6 months ago - 14.7 thousand downloads total - 9 stars on GitHub - 1 maintainer
TDbasedUFEadv 1.2.0
Advanced package of tensor decomposition based unsupervised feature extraction3 versions - Latest release: 6 months ago - 1.55 thousand downloads total - 0 stars on GitHub - 1 maintainer
deco 1.18.0 removed
Decomposing Heterogeneous Cohorts using Omic Data Profiling2 versions - Latest release: 6 months ago - 4.59 thousand downloads total - 4 stars on GitHub - 1 maintainer
rnaEditr 1.12.0
Statistical analysis of RNA editing sites and hyper-editing regions3 versions - Latest release: 6 months ago - 3.35 thousand downloads total - 3 stars on GitHub - 1 maintainer
biosigner 1.30.0
Signature discovery from omics data3 versions - Latest release: 6 months ago - 2 dependent packages - 14.2 thousand downloads total - 1 maintainer
sarks 1.14.0
Suffix Array Kernel Smoothing for discovery of correlative sequence motifs and multi-motif domains3 versions - Latest release: 6 months ago - 4.04 thousand downloads total - 1 maintainer
FCBF 2.10.0
Fast Correlation Based Filter for Feature Selection3 versions - Latest release: 6 months ago - 1 dependent package - 7.45 thousand downloads total - 1 maintainer
TADCompare 1.12.1
TADCompare: Identification and characterization of differential TADs4 versions - Latest release: 2 months ago - 5.22 thousand downloads total - 19 stars on GitHub - 1 maintainer
BUScorrect 1.20.0
Batch Effects Correction with Unknown Subtypes3 versions - Latest release: 6 months ago - 6.23 thousand downloads total - 1 maintainer
iasva 1.20.0
Iteratively Adjusted Surrogate Variable Analysis3 versions - Latest release: 6 months ago - 6.5 thousand downloads total - 2 maintainers
evaluomeR 1.20.0
Evaluation of Bioinformatics Metrics3 versions - Latest release: 15 days ago - 5.61 thousand downloads total - 0 stars on GitHub - 1 maintainer
trena 1.24.0 removed
Fit transcriptional regulatory networks using gene expression, priors, machine learning2 versions - Latest release: 6 months ago - 7 thousand downloads total - 1 stars on GitHub - 1 maintainer
BUSseq 1.8.0
Batch Effect Correction with Unknow Subtypes for scRNA-seq data3 versions - Latest release: 6 months ago - 2.52 thousand downloads total - 0 stars on GitHub - 1 maintainer
diffcyt 1.22.1
Differential discovery in high-dimensional cytometry via high-resolution clustering4 versions - Latest release: about 1 month ago - 5 dependent packages - 26.6 thousand downloads total - 18 stars on GitHub - 1 maintainer
monaLisa 1.10.0
Binned Motif Enrichment Analysis and Visualization4 versions - Latest release: 10 days ago - 5.13 thousand downloads total - 30 stars on GitHub - 1 maintainer
Top 9.4% on bioconductor.org
4 versions - Latest release: 10 days ago - 20.1 thousand downloads total - 160 stars on GitHub - 1 maintainer
MicrobiotaProcess 1.16.0
A comprehensive R package for managing and analyzing microbiome and other ecological data within ...4 versions - Latest release: 10 days ago - 20.1 thousand downloads total - 160 stars on GitHub - 1 maintainer
retrofit 1.4.0
RETROFIT: Reference-free deconvolution of cell mixtures in spatial transcriptomics3 versions - Latest release: 20 days ago - 1.07 thousand downloads total - 4 stars on GitHub - 1 maintainer
raer 1.2.0
RNA editing tools in R3 versions - Latest release: 8 days ago - 823 downloads total - 6 stars on GitHub - 1 maintainer
CaDrA 1.2.0
Candidate Driver Analysis4 versions - Latest release: 9 days ago - 825 downloads total - 24 stars on GitHub - 1 maintainer
iSEEu 1.15.1
iSEE Universe3 versions - Latest release: 20 days ago - 1 dependent package - 6.84 thousand downloads total - 10 stars on GitHub - 1 maintainer
Top 5.5% on bioconductor.org
3 versions - Latest release: 20 days ago - 8 dependent packages - 33.6 thousand downloads total - 218 stars on GitHub - 1 maintainer
iSEE 2.16.0
Interactive SummarizedExperiment Explorer3 versions - Latest release: 20 days ago - 8 dependent packages - 33.6 thousand downloads total - 218 stars on GitHub - 1 maintainer
SpatialDecon 1.14.0
Deconvolution of mixed cells from spatial and/or bulk gene expression data4 versions - Latest release: 10 days ago - 1 dependent package - 8.19 thousand downloads total - 27 stars on GitHub - 1 maintainer
timeOmics 1.16.0
Time-Course Multi-Omics data integration3 versions - Latest release: 13 days ago - 1 dependent package - 5.04 thousand downloads total - 21 stars on GitHub - 1 maintainer
Top 5.6% on bioconductor.org
3 versions - Latest release: 13 days ago - 42.3 thousand downloads total - 1 maintainer
RDRToolbox 1.54.0
A package for nonlinear dimension reduction with Isomap and LLE.3 versions - Latest release: 13 days ago - 42.3 thousand downloads total - 1 maintainer
martini 1.24.0
GWAS Incorporating Networks3 versions - Latest release: 13 days ago - 7.58 thousand downloads total - 4 stars on GitHub - 1 maintainer
seqArchR 1.8.0
Identify Different Architectures of Sequence Elements3 versions - Latest release: 16 days ago - 1 dependent package - 2.62 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 6.9% on bioconductor.org
3 versions - Latest release: 18 days ago - 1 dependent package - 40.7 thousand downloads total - 27 stars on GitHub - 1 maintainer
M3Drop 1.30.0
Michaelis-Menten Modelling of Dropouts in single-cell RNASeq3 versions - Latest release: 18 days ago - 1 dependent package - 40.7 thousand downloads total - 27 stars on GitHub - 1 maintainer
consICA 2.2.0
consensus Independent Component Analysis3 versions - Latest release: 20 days ago - 2.29 thousand downloads total - 0 stars on GitHub - 1 maintainer
iSEEfier 1.0.0
Streamlining the creation of initial states for starting an iSEE instance1 version - Latest release: 21 days ago - 73 downloads total - 0 stars on GitHub - 1 maintainer
ClusterFoldSimilarity 1.0.0
Calculate similarity of clusters from different single cell samples using foldchanges1 version - Latest release: 21 days ago - 180 downloads total - 1 maintainer
censcyt 1.10.0
Differential abundance analysis with a right censored covariate in high-dimensional cytometry2 versions - Latest release: 6 months ago - 3.07 thousand downloads total - 0 stars on GitHub - 1 maintainer
SpectralTAD 1.18.0
SpectralTAD: Hierarchical TAD detection using spectral clustering2 versions - Latest release: 6 months ago - 1 dependent package - 6.76 thousand downloads total - 6 stars on GitHub - 1 maintainer
preciseTAD 1.12.0
preciseTAD: A machine learning framework for precise TAD boundary prediction2 versions - Latest release: 6 months ago - 3.45 thousand downloads total - 6 stars on GitHub - 1 maintainer
rCGH 1.32.0
Comprehensive Pipeline for Analyzing and Visualizing Array-Based CGH Data2 versions - Latest release: 6 months ago - 1 dependent package - 15.6 thousand downloads total - 4 stars on GitHub - 1 maintainer
pathwayPCA 1.18.0
Integrative Pathway Analysis with Modern PCA Methodology and Gene Selection2 versions - Latest release: 6 months ago - 1 dependent package - 7.17 thousand downloads total - 11 stars on GitHub - 1 maintainer
MOMA 1.14.0
Multi Omic Master Regulator Analysis2 versions - Latest release: 6 months ago - 4.35 thousand downloads total - 5 stars on GitHub - 1 maintainer
GeneAccord 1.18.0 removed
Detection of clonally exclusive gene or pathway pairs in a cohort of cancer patients1 version - Latest release: 7 months ago - 4.41 thousand downloads total - 2 stars on GitHub - 1 maintainer
Related Keywords
Software
60
GeneExpression
28
Clustering
26
Sequencing
21
ImmunoOncology
20
Transcriptomics
19
RNASeq
18
Classification
18
SingleCell
17
Visualization
11
DimensionReduction
11
Regression
11
Transcription
11
DifferentialExpression
9
Genetics
9
Proteomics
8
SystemsBiology
8
Microarray
8
Bayesian
8
GeneRegulation
7
StatisticalMethod
7
CellBasedAssays
7
MultipleComparison
7
Epigenetics
6
r
6
Coverage
6
DNAMethylation
5
FunctionalGenomics
5
bioinformatics
5
Preprocessing
5
Survival
5
GeneticVariability
4
BiomedicalInformatics
4
GeneTarget
4
BatchEffect
4
FlowCytometry
4
GUI
3
CellBiology
3
Normalization
3
clustering
3
HiC
3
single-cell
3
Metabolomics
3
QualityControl
3
Pathways
3
Alignment
3
SomaticMutation
3
GenePrediction
3
DataRepresentation
3
Network
3
GraphAndNetwork
3
rna-seq
2
rna-seq-analysis
2
MotifDiscovery
2
transcriptomics
2
r-package
2
DataImport
2
GO
2
Lipidomics
2
Annotation
2
GeneSetEnrichment
2
ShinyApps
2
SNP
2
Technology
2
genomics
2
MethylationArray
2
GenomeWideAssociation
2
human-cell-atlas
2
tensor-decomposition
2
bioconductor-package
2
Metagenomics
2
MassSpectrometry
2
DifferentialMethylation
2
KEGG
2
GenomicVariation
2
Spatial
2
Microbiome
2
heterogeneity
2
mRNAMicroarray
2
CopyNumberVariation
2
DNASeq
2
single-cell-rna-seq
2
NetworkInference
2
hacktoberfest
2
MathematicalBiology
2
rstats
1
gui
1
shiny
1
gene-expression
1
visualization
1
feature-extraction
1
dimension-reduction
1
cooccurrence
1
Epitranscriptomics
1
single-cell-analysis
1
exclusivity
1
mutual
1
PrincipalComponent
1
GeneSignaling
1
aCGH
1