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bioconductor.org packages

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eds 1.4.0
eds: Low-level reader for Alevin EDS format
2 versions - Latest release: 6 months ago - 2 dependent packages - 12.6 thousand downloads total - 0 stars on GitHub - 1 maintainer
meshr 2.8.0
Tools for conducting enrichment analysis of MeSH
2 versions - Latest release: 6 months ago - 1 dependent package - 24.4 thousand downloads total - 0 stars on GitHub - 1 maintainer
RESOLVE 1.6.0
RESOLVE: An R package for the efficient analysis of mutational signatures from cancer genomes
3 versions - Latest release: 4 days ago - 1.58 thousand downloads total - 0 stars on GitHub - 1 maintainer
pageRank 1.14.0
Temporal and Multiplex PageRank for Gene Regulatory Network Analysis
3 versions - Latest release: 1 day ago - 3.5 thousand downloads total - 0 stars on GitHub - 1 maintainer
Director 1.28.0
A dynamic visualization tool of multi-level data
2 versions - Latest release: 6 months ago - 8.25 thousand downloads total - 0 stars on GitHub - 1 maintainer
BASiCStan 1.4.0
Stan implementation of BASiCS
2 versions - Latest release: 6 months ago - 1.37 thousand downloads total - 0 stars on GitHub - 1 maintainer
DMCHMM 1.24.0
Differentially Methylated CpG using Hidden Markov Model
2 versions - Latest release: 6 months ago - 8.33 thousand downloads total - 0 stars on GitHub - 1 maintainer
ClusterSignificance 1.30.0
The ClusterSignificance package provides tools to assess if class clusters in dimensionality redu...
2 versions - Latest release: 6 months ago - 10.7 thousand downloads total - 0 stars on GitHub - 1 maintainer
evaluomeR 1.20.0
Evaluation of Bioinformatics Metrics
3 versions - Latest release: 3 days ago - 5.5 thousand downloads total - 0 stars on GitHub - 1 maintainer
simpleSeg 1.6.0
A package to perform simple cell segmentation
4 versions - Latest release: about 21 hours ago - 1.85 thousand downloads total - 0 stars on GitHub - 1 maintainer
CellBarcode 1.8.1
Cellular DNA Barcode Analysis toolkit
3 versions - Latest release: about 2 months ago - 2.15 thousand downloads total - 0 stars on GitHub - 1 maintainer
smartid 1.0.0
Scoring and Marker Selection Method Based on Modified TF-IDF
1 version - Latest release: 9 days ago - 185 downloads total - 0 stars on GitHub - 1 maintainer
SARC 1.0.0
Statistical Analysis of Regions with CNVs
1 version - Latest release: 7 months ago - 634 downloads total - 0 stars on GitHub - 1 maintainer
TENxIO 1.5.4
Import methods for 10X Genomics files
3 versions - Latest release: 9 days ago - 1.5 thousand downloads total - 0 stars on GitHub - 1 maintainer
combi 1.14.0
Compositional omics model based visual integration
2 versions - Latest release: 6 months ago - 4.06 thousand downloads total - 0 stars on GitHub - 1 maintainer
selectKSigs 1.14.0
Selecting the number of mutational signatures using a perplexity-based measure and cross-validation
2 versions - Latest release: 6 months ago - 3.85 thousand downloads total - 0 stars on GitHub - 1 maintainer
DELocal 1.4.0
Identifies differentially expressed genes with respect to other local genes
4 versions - Latest release: 5 days ago - 1.06 thousand downloads total - 0 stars on GitHub - 1 maintainer
cyanoFilter 1.10.0
Phytoplankton Population Identification using Cell Pigmentation and/or Complexity
2 versions - Latest release: 6 months ago - 2.5 thousand downloads total - 0 stars on GitHub - 1 maintainer
iSEEhex 1.6.0
iSEE extension for summarising data points in hexagonal bins
3 versions - Latest release: 1 day ago - 1 dependent package - 3.36 thousand downloads total - 0 stars on GitHub - 1 maintainer
mitoClone2 1.10.0
Clonal Population Identification in Single-Cell RNA-Seq Data using Mitochondrial and Somatic Muta...
4 versions - Latest release: 1 day ago - 2.32 thousand downloads total - 0 stars on GitHub - 1 maintainer
pengls 1.8.0
Fit Penalised Generalised Least Squares models
2 versions - Latest release: 6 months ago - 1.67 thousand downloads total - 0 stars on GitHub - 1 maintainer
brainflowprobes 1.18.0
Plots and annotation for choosing BrainFlow target probe sequence
3 versions - Latest release: 8 days ago - 4.96 thousand downloads total - 0 stars on GitHub - 1 maintainer
hdxmsqc 1.0.0
An R package for quality Control for hydrogen deuterium exchange mass spectrometry experiments
1 version - Latest release: 9 days ago - 0 stars on GitHub - 1 maintainer
dinoR 1.0.0
Differential NOMe-seq analysis
1 version - Latest release: 9 days ago - 145 downloads total - 0 stars on GitHub - 1 maintainer
smoothclust 0.99.8
smoothclust
1 version - Latest release: 9 days ago - 162 downloads total - 0 stars on GitHub - 1 maintainer
limpca 1.0.0
An R package for the linear modeling of high-dimensional designed data based on ASCA/APCA family ...
1 version - Latest release: 9 days ago - 0 stars on GitHub - 1 maintainer
Damsel 1.0.0
Damsel: an end to end analysis of DamID
1 version - Latest release: 9 days ago - 0 stars on GitHub - 1 maintainer
spoon 0.99.10
Address the Mean-variance Relationship in Spatial Transcriptomics Data
1 version - Latest release: 9 days ago - 154 downloads total - 0 stars on GitHub - 1 maintainer
scMitoMut 1.0.0
Single-cell Mitochondrial Mutation Analysis Tool
1 version - Latest release: 9 days ago - 171 downloads total - 0 stars on GitHub - 1 maintainer
BREW3R.r 1.0.0
R package associated to BREW3R
1 version - Latest release: 9 days ago - 0 stars on GitHub - 1 maintainer
simPIC 1.0.0
simPIC: flexible simulation of paired-insertion counts for single-cell ATAC-sequencing data
1 version - Latest release: 9 days ago - 148 downloads total - 0 stars on GitHub - 1 maintainer
SpotSweeper 0.99.5
Spatially-aware quality control for spatial transcriptomics
1 version - Latest release: 9 days ago - 0 stars on GitHub - 1 maintainer
tpSVG 0.99.7
Thin plate models to detect spatially variable genes
1 version - Latest release: 9 days ago - 151 downloads total - 0 stars on GitHub - 1 maintainer
saseR 1.0.0
Scalable Aberrant Splicing and Expression Retrieval
1 version - Latest release: 9 days ago - 179 downloads total - 0 stars on GitHub - 1 maintainer
findIPs 1.0.0
Influential Points Detection for Feature Rankings
1 version - Latest release: 9 days ago - 0 stars on GitHub - 1 maintainer
VisiumIO 1.0.0
Import Visium data from the 10X Space Ranger pipeline
1 version - Latest release: 9 days ago - 169 downloads total - 0 stars on GitHub - 1 maintainer
epiregulon.extra 1.0.0
Companion package to epiregulon with additional plotting, differential and graph functions
1 version - Latest release: 9 days ago - 0 stars on GitHub - 1 maintainer
SurfR 0.99.54
Surface Protein Prediction and Identification
1 version - Latest release: 9 days ago - 129 downloads total - 0 stars on GitHub - 1 maintainer
methodical 1.0.0
Discovering genomic regions where methylation is strongly associated with transcriptional activity
1 version - Latest release: 9 days ago - 158 downloads total - 0 stars on GitHub - 1 maintainer
iSEEfier 1.0.0
Streamlining the creation of initial states for starting an iSEE instance
1 version - Latest release: 9 days ago - 73 downloads total - 0 stars on GitHub - 1 maintainer
MAPFX 1.0.0
MAssively Parallel Flow cytometry Xplorer (MAPFX): A Toolbox for Analysing Data from the Massivel...
1 version - Latest release: 9 days ago - 0 stars on GitHub - 1 maintainer
mosdef 1.0.0
MOSt frequently used and useful Differential Expression Functions
1 version - Latest release: 9 days ago - 0 stars on GitHub - 1 maintainer
SpaceMarkers 1.0.0
Spatial Interaction Markers
1 version - Latest release: 9 days ago - 112 downloads total - 0 stars on GitHub - 1 maintainer
HybridExpress 1.0.0
Comparative analysis of RNA-seq data for hybrids and their progenitors
1 version - Latest release: 9 days ago - 143 downloads total - 0 stars on GitHub - 1 maintainer
affyPLM 1.78.0
Methods for fitting probe-level models
2 versions - Latest release: 6 months ago - 9 dependent packages - 568 thousand downloads total - 0 stars on GitHub - 1 maintainer
cypress 1.0.0
Cell-Type-Specific Power Assessment
1 version - Latest release: 9 days ago - 118 downloads total - 0 stars on GitHub - 1 maintainer
UPDhmm 1.0.0
Detecting Uniparental Disomy through NGS trio data
1 version - Latest release: 9 days ago - 0 stars on GitHub - 1 maintainer
multistateQTL 1.0.0
Toolkit for the analysis of multi-state QTL data
1 version - Latest release: 9 days ago - 0 stars on GitHub - 1 maintainer
motifTestR 1.0.0
Perform key tests for binding motifs in sequence data
1 version - Latest release: 9 days ago - 179 downloads total - 0 stars on GitHub - 1 maintainer
MIRit 0.99.13
Integrate microRNA and gene expression to decipher pathway complexity
1 version - Latest release: 9 days ago - 151 downloads total - 0 stars on GitHub - 1 maintainer
Pedixplorer 1.0.0
Pedigree Functions
1 version - Latest release: 9 days ago - 169 downloads total - 0 stars on GitHub - 1 maintainer
PIPETS 1.0.0
Poisson Identification of PEaks from Term-Seq data
1 version - Latest release: 9 days ago - 175 downloads total - 0 stars on GitHub - 1 maintainer
MIGSA 1.24.0 removed
Massive and Integrative Gene Set Analysis
1 version - Latest release: 7 months ago - 7.89 thousand downloads total - 0 stars on GitHub - 1 maintainer
EpiTxDb 1.14.1
Storing and accessing epitranscriptomic information using the AnnotationDbi interface
3 versions - Latest release: 4 months ago - 4.66 thousand downloads total - 0 stars on GitHub - 1 maintainer
GBScleanR 1.8.0
Error correction tool for noisy genotyping by sequencing (GBS) data
3 versions - Latest release: 7 days ago - 2.08 thousand downloads total - 0 stars on GitHub - 1 maintainer
cytoKernel 1.8.0
Differential expression using kernel-based score test
2 versions - Latest release: 6 months ago - 1.96 thousand downloads total - 0 stars on GitHub - 1 maintainer
TOP 1.2.0
TOP Constructs Transferable Model Across Gene Expression Platforms
2 versions - Latest release: 6 months ago - 855 downloads total - 0 stars on GitHub - 1 maintainer
hoodscanR 1.0.0
Spatial cellular neighbourhood scanning in R
1 version - Latest release: 7 months ago - 577 downloads total - 0 stars on GitHub - 1 maintainer
cola 2.8.0
A Framework for Consensus Partitioning
2 versions - Latest release: 6 months ago - 2 dependent packages - 9.07 thousand downloads total - 0 stars on GitHub - 1 maintainer
TBSignatureProfiler 1.14.0
Profile RNA-Seq Data Using TB Pathway Signatures
2 versions - Latest release: 6 months ago - 4.33 thousand downloads total - 0 stars on GitHub - 1 maintainer
chihaya 1.2.0
Save Delayed Operations to a HDF5 File
2 versions - Latest release: 6 months ago - 1 dependent package - 1.19 thousand downloads total - 0 stars on GitHub - 1 maintainer
IntOMICS 1.2.0
Integrative analysis of multi-omics data to infer regulatory networks
2 versions - Latest release: 6 months ago - 914 downloads total - 0 stars on GitHub - 1 maintainer
RIPAT 1.12.0
Retroviral Integration Pattern Analysis Tool (RIPAT)
2 versions - Latest release: 6 months ago - 2.77 thousand downloads total - 0 stars on GitHub - 1 maintainer
ramr 1.10.0
Detection of Rare Aberrantly Methylated Regions in Array and NGS Data
2 versions - Latest release: 6 months ago - 2.63 thousand downloads total - 0 stars on GitHub - 1 maintainer
methylInheritance 1.26.0
Permutation-Based Analysis associating Conserved Differentially Methylated Elements Across Multip...
2 versions - Latest release: 6 months ago - 1 dependent package - 9.03 thousand downloads total - 0 stars on GitHub - 1 maintainer
Rvisdiff 1.0.0
Interactive Graphs for Differential Expression
1 version - Latest release: 7 months ago - 466 downloads total - 0 stars on GitHub - 1 maintainer
BufferedMatrix 1.66.0
A matrix data storage object held in temporary files
2 versions - Latest release: 6 months ago - 1 dependent package - 32.9 thousand downloads total - 0 stars on GitHub - 1 maintainer
multicrispr 1.12.9
Multi-locus multi-purpose Crispr/Cas design
3 versions - Latest release: 28 days ago - 3.78 thousand downloads total - 0 stars on GitHub - 1 maintainer
rsemmed 1.12.0
An interface to the Semantic MEDLINE database
2 versions - Latest release: 6 months ago - 3.1 thousand downloads total - 0 stars on GitHub - 1 maintainer
FamAgg 1.30.0
Pedigree Analysis and Familial Aggregation
2 versions - Latest release: 6 months ago - 12.2 thousand downloads total - 0 stars on GitHub - 1 maintainer
tRNA 1.20.1
Analyzing tRNA sequences and structures
3 versions - Latest release: 3 months ago - 2 dependent packages - 8.55 thousand downloads total - 0 stars on GitHub - 1 maintainer
roastgsa 1.0.0
Rotation based gene set analysis
1 version - Latest release: 7 months ago - 569 downloads total - 0 stars on GitHub - 1 maintainer
cytoMEM 1.6.0
Marker Enrichment Modeling (MEM)
2 versions - Latest release: 6 months ago - 2.09 thousand downloads total - 0 stars on GitHub - 1 maintainer
scDDboost 1.4.0
A compositional model to assess expression changes from single-cell rna-seq data
2 versions - Latest release: 6 months ago - 1.26 thousand downloads total - 0 stars on GitHub - 1 maintainer
PFP 1.10.0
Pathway Fingerprint Framework in R
2 versions - Latest release: 6 months ago - 1.82 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 3.5% on bioconductor.org
Heatplus 3.12.0
Heatmaps with row and/or column covariates and colored clusters
3 versions - Latest release: about 11 hours ago - 2 dependent packages - 133 thousand downloads total - 0 stars on GitHub - 1 maintainer
pairkat 1.8.0
PaIRKAT
2 versions - Latest release: 6 months ago - 1.79 thousand downloads total - 0 stars on GitHub - 1 maintainer
ROCpAI 1.14.0
Receiver Operating Characteristic Partial Area Indexes for evaluating classifiers
2 versions - Latest release: 6 months ago - 3.67 thousand downloads total - 0 stars on GitHub - 1 maintainer
HiCool 1.2.0
HiCool
2 versions - Latest release: 6 months ago - 1.22 thousand downloads total - 0 stars on GitHub - 1 maintainer
bcSeq 1.24.0
Fast Sequence Mapping in High-Throughput shRNA and CRISPR Screens
2 versions - Latest release: 6 months ago - 7.8 thousand downloads total - 0 stars on GitHub - 1 maintainer
IntramiRExploreR 1.24.0
Predicting Targets for Drosophila Intragenic miRNAs
2 versions - Latest release: 6 months ago - 6.58 thousand downloads total - 0 stars on GitHub - 1 maintainer
CIMICE 1.10.0
CIMICE-R: (Markov) Chain Method to Inferr Cancer Evolution
2 versions - Latest release: 6 months ago - 2.67 thousand downloads total - 0 stars on GitHub - 1 maintainer
SeqGate 1.12.0
Filtering of Lowly Expressed Features
2 versions - Latest release: 6 months ago - 4.59 thousand downloads total - 0 stars on GitHub - 1 maintainer
cellmigRation 1.10.0
Track Cells, Analyze Cell Trajectories and Compute Migration Statistics
2 versions - Latest release: 7 months ago - 2.69 thousand downloads total - 0 stars on GitHub - 1 maintainer
plyinteractions 1.0.0
Extending tidy verbs to genomic interactions
2 versions - Latest release: 6 months ago - 665 downloads total - 0 stars on GitHub - 1 maintainer
MSstatsLOBD 1.10.0
Assay characterization: estimation of limit of blanc(LoB) and limit of detection(LOD)
2 versions - Latest release: 6 months ago - 2.47 thousand downloads total - 0 stars on GitHub - 1 maintainer
blacksheepr 1.16.0
Outlier Analysis for pairwise differential comparison
2 versions - Latest release: 6 months ago - 5.2 thousand downloads total - 0 stars on GitHub - 1 maintainer
DelayedRandomArray 1.10.0
Delayed Arrays of Random Values
2 versions - Latest release: 6 months ago - 1 dependent package - 3.14 thousand downloads total - 0 stars on GitHub - 1 maintainer
tadar 1.0.0
Transcriptome Analysis of Differential Allelic Representation
1 version - Latest release: 7 months ago - 652 downloads total - 0 stars on GitHub - 1 maintainer
antiProfiles 1.42.0
Implementation of gene expression anti-profiles
2 versions - Latest release: 6 months ago - 20.9 thousand downloads total - 0 stars on GitHub - 1 maintainer
ipdDb 1.20.0
IPD IMGT/HLA and IPD KIR database for Homo sapiens
2 versions - Latest release: 6 months ago - 6.52 thousand downloads total - 0 stars on GitHub - 1 maintainer
Motif2Site 1.6.0
Detect binding sites from motifs and ChIP-seq experiments, and compare binding sites across condi...
2 versions - Latest release: 6 months ago - 1.64 thousand downloads total - 0 stars on GitHub - 1 maintainer
compSPOT 1.0.0
compSPOT: Tool for identifying and comparing significantly mutated genomic hotspots
1 version - Latest release: 7 months ago - 563 downloads total - 0 stars on GitHub - 1 maintainer
ADImpute 1.12.0
Adaptive Dropout Imputer (ADImpute)
2 versions - Latest release: 6 months ago - 4.7 thousand downloads total - 0 stars on GitHub - 1 maintainer
TDbasedUFEadv 1.2.0
Advanced package of tensor decomposition based unsupervised feature extraction
2 versions - Latest release: 6 months ago - 1.19 thousand downloads total - 0 stars on GitHub - 1 maintainer
RJMCMCNucleosomes 1.26.0
Bayesian hierarchical model for genome-wide nucleosome positioning with high-throughput short-rea...
2 versions - Latest release: 6 months ago - 8.66 thousand downloads total - 0 stars on GitHub - 1 maintainer
cytofQC 1.4.0
Labels normalized cells for CyTOF data and assigns probabilities for each label
3 versions - Latest release: 8 days ago - 1.15 thousand downloads total - 0 stars on GitHub - 1 maintainer
randRotation 1.14.0
Random Rotation Methods for High Dimensional Data with Batch Structure
2 versions - Latest release: 6 months ago - 3.53 thousand downloads total - 0 stars on GitHub - 1 maintainer
AnVILBilling 1.12.0
Provide functions to retrieve and report on usage expenses in NHGRI AnVIL (anvilproject.org).
2 versions - Latest release: 6 months ago - 3.26 thousand downloads total - 0 stars on GitHub - 1 maintainer
magpie 1.2.0
MeRIP-Seq data Analysis for Genomic Power Investigation and Evaluation
2 versions - Latest release: 6 months ago - 927 downloads total - 0 stars on GitHub - 1 maintainer