bioconductor.org "Software" keyword
View the packages on the bioconductor.org package registry that are tagged with the "Software" keyword.
spARI 1.0.0
Spatially Aware Adjusted Rand Index for Evaluating Spatial Transcritpomics Clustering1 version - Latest release: 2 months ago - 662 downloads total - 1 maintainer
Top 1.7% on bioconductor.org
11 versions - Latest release: 29 days ago - 69 dependent packages - 3.18 million downloads total - 69 stars on GitHub - 1 maintainer
rhdf5 2.54.1
R Interface to HDF511 versions - Latest release: 29 days ago - 69 dependent packages - 3.18 million downloads total - 69 stars on GitHub - 1 maintainer
gpuMagic 1.25.1
An openCL compiler with the capacity to compile R functions and run the code on GPU6 versions - Latest release: 2 months ago - 10.3 thousand downloads total - 10 stars on GitHub - 1 maintainer
seqArchRplus 1.9.0
Downstream analyses of promoter sequence architectures and HTML report generation6 versions - Latest release: about 1 month ago - 5.73 thousand downloads total - 1 stars on GitHub - 1 maintainer
iscream 1.0.0
Make fast and memory efficient BED file queries, summaries and matrices1 version - Latest release: 2 months ago - 483 downloads total - 0 stars on GitHub - 1 maintainer
Top 0.1% on bioconductor.org
7 versions - Latest release: 2 months ago - 729 dependent packages - 11.7 million downloads total - 1 maintainer
BiocGenerics 0.56.0
S4 generic functions used in Bioconductor7 versions - Latest release: 2 months ago - 729 dependent packages - 11.7 million downloads total - 1 maintainer
scDotPlot 1.4.0
Cluster a Single-cell RNA-seq Dot Plot5 versions - Latest release: about 1 month ago - 4.42 thousand downloads total - 7 stars on GitHub - 1 maintainer
SpaNorm 1.4.0
Spatially-aware normalisation for spatial transcriptomics data3 versions - Latest release: about 1 month ago - 3.68 thousand downloads total - 13 stars on GitHub - 1 maintainer
Top 1.5% on bioconductor.org
9 versions - Latest release: 2 months ago - 96 dependent packages - 1.03 million downloads total - 1 maintainer
scater 1.38.0
Single-Cell Analysis Toolkit for Gene Expression Data in R9 versions - Latest release: 2 months ago - 96 dependent packages - 1.03 million downloads total - 1 maintainer
GIGSEA 1.28.0
Genotype Imputed Gene Set Enrichment Analysis6 versions - Latest release: about 1 month ago - 11 thousand downloads total - 1 maintainer
Top 1.9% on bioconductor.org
8 versions - Latest release: 2 months ago - 31 dependent packages - 930 thousand downloads total - 64 stars on GitHub - 1 maintainer
minfi 1.56.0
Analyze Illumina Infinium DNA methylation arrays8 versions - Latest release: 2 months ago - 31 dependent packages - 930 thousand downloads total - 64 stars on GitHub - 1 maintainer
Top 1.8% on bioconductor.org
6 versions - Latest release: 2 months ago - 10 dependent packages - 402 thousand downloads total - 1 maintainer
lumi 2.62.0
BeadArray Specific Methods for Illumina Methylation and Expression Microarrays6 versions - Latest release: 2 months ago - 10 dependent packages - 402 thousand downloads total - 1 maintainer
Top 1.4% on bioconductor.org
7 versions - Latest release: 2 months ago - 49 dependent packages - 1.36 million downloads total - 1 maintainer
GSEABase 1.72.0
Gene set enrichment data structures and methods7 versions - Latest release: 2 months ago - 49 dependent packages - 1.36 million downloads total - 1 maintainer
Top 0.2% on bioconductor.org
21 versions - Latest release: 29 days ago - 342 dependent packages - 10.5 million downloads total - 1 maintainer
GenomeInfoDb 1.46.2
Utilities for manipulating chromosome names, including modifying them to follow a particular nami...21 versions - Latest release: 29 days ago - 342 dependent packages - 10.5 million downloads total - 1 maintainer
CeTF 1.22.0
Coexpression for Transcription Factors using Regulatory Impact Factors and Partial Correlation an...6 versions - Latest release: about 1 month ago - 12.6 thousand downloads total - 1 maintainer
Top 1.4% on bioconductor.org
6 versions - Latest release: 2 months ago - 45 dependent packages - 2.32 million downloads total - 106 stars on GitHub - 2 maintainers
qvalue 2.42.0
Q-value estimation for false discovery rate control6 versions - Latest release: 2 months ago - 45 dependent packages - 2.32 million downloads total - 106 stars on GitHub - 2 maintainers
Top 0.7% on bioconductor.org
8 versions - Latest release: 26 days ago - 101 dependent packages - 3.41 million downloads total - 1 maintainer
graph 1.88.1
graph: A package to handle graph data structures8 versions - Latest release: 26 days ago - 101 dependent packages - 3.41 million downloads total - 1 maintainer
Top 0.9% on bioconductor.org
8 versions - Latest release: 2 months ago - 93 dependent packages - 2.03 million downloads total - 1 maintainer
VariantAnnotation 1.56.0
Annotation of Genetic Variants8 versions - Latest release: 2 months ago - 93 dependent packages - 2.03 million downloads total - 1 maintainer
soGGi 1.41.1
Visualise ChIP-seq, MNase-seq and motif occurrence as aggregate plots Summarised Over Grouped Gen...7 versions - Latest release: about 1 month ago - 1 dependent package - 44 thousand downloads total - 1 maintainer
Top 0.7% on bioconductor.org
6 versions - Latest release: 2 months ago - 66 dependent packages - 4.11 million downloads total - 1 maintainer
genefilter 1.92.0
genefilter: methods for filtering genes from high-throughput experiments6 versions - Latest release: 2 months ago - 66 dependent packages - 4.11 million downloads total - 1 maintainer
compcodeR 1.46.0
RNAseq data simulation, differential expression analysis and performance comparison of differenti...6 versions - Latest release: about 1 month ago - 32.4 thousand downloads total - 12 stars on GitHub - 1 maintainer
multistateQTL 2.2.0
Toolkit for the analysis of multi-state QTL data5 versions - Latest release: about 2 months ago - 4.55 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 1.4% on bioconductor.org
6 versions - Latest release: 2 months ago - 47 dependent packages - 2.3 million downloads total - 103 stars on GitHub - 1 maintainer
GEOquery 2.78.0
Get data from NCBI Gene Expression Omnibus (GEO)6 versions - Latest release: 2 months ago - 47 dependent packages - 2.3 million downloads total - 103 stars on GitHub - 1 maintainer
Top 1.7% on bioconductor.org
11 versions - Latest release: 15 days ago - 28 dependent packages - 2.14 million downloads total - 1 maintainer
ggtree 4.0.3
an R package for visualization of tree and annotation data11 versions - Latest release: 15 days ago - 28 dependent packages - 2.14 million downloads total - 1 maintainer
Top 0.9% on bioconductor.org
6 versions - Latest release: 2 months ago - 74 dependent packages - 2.22 million downloads total - 1 maintainer
affy 1.88.0
Methods for Affymetrix Oligonucleotide Arrays6 versions - Latest release: 2 months ago - 74 dependent packages - 2.22 million downloads total - 1 maintainer
Top 0.9% on bioconductor.org
6 versions - Latest release: 2 months ago - 36 dependent packages - 9.2 million downloads total - 1 maintainer
XVector 0.50.0
Foundation of external vector representation and manipulation in Bioconductor6 versions - Latest release: 2 months ago - 36 dependent packages - 9.2 million downloads total - 1 maintainer
Top 1.5% on bioconductor.org
13 versions - Latest release: 2 months ago - 15 dependent packages - 962 thousand downloads total - 185 stars on GitHub - 1 maintainer
xcms 4.8.0
LC-MS and GC-MS Data Analysis13 versions - Latest release: 2 months ago - 15 dependent packages - 962 thousand downloads total - 185 stars on GitHub - 1 maintainer
Top 0.8% on bioconductor.org
8 versions - Latest release: 2 months ago - 129 dependent packages - 2.73 million downloads total - 1 maintainer
BSgenome 1.78.0
Software infrastructure for efficient representation of full genomes and their SNPs8 versions - Latest release: 2 months ago - 129 dependent packages - 2.73 million downloads total - 1 maintainer
LoomExperiment 1.28.0
LoomExperiment container7 versions - Latest release: about 1 month ago - 2 dependent packages - 47.8 thousand downloads total - 1 maintainer
Top 0.6% on bioconductor.org
26 versions - Latest release: 8 days ago - 181 dependent packages - 4.18 million downloads total - 4 maintainers
edgeR 4.8.2
Empirical Analysis of Digital Gene Expression Data in R26 versions - Latest release: 8 days ago - 181 dependent packages - 4.18 million downloads total - 4 maintainers
Top 1.0% on bioconductor.org
6 versions - Latest release: 2 months ago - 61 dependent packages - 1.9 million downloads total - 1 maintainer
Rgraphviz 2.54.0
Provides plotting capabilities for R graph objects6 versions - Latest release: 2 months ago - 61 dependent packages - 1.9 million downloads total - 1 maintainer
cola 2.16.0
A Framework for Consensus Partitioning6 versions - Latest release: 2 months ago - 2 dependent packages - 21.4 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 0.2% on bioconductor.org
11 versions - Latest release: 2 months ago - 333 dependent packages - 9.17 million downloads total - 1 maintainer
Biostrings 2.78.0
Efficient manipulation of biological strings11 versions - Latest release: 2 months ago - 333 dependent packages - 9.17 million downloads total - 1 maintainer
Top 1.5% on bioconductor.org
7 versions - Latest release: 29 days ago - 481 thousand downloads total - 384 stars on GitHub - 1 maintainer
EnhancedVolcano 1.28.2
Publication-ready volcano plots with enhanced colouring and labeling7 versions - Latest release: 29 days ago - 481 thousand downloads total - 384 stars on GitHub - 1 maintainer
Top 0.1% on bioconductor.org
8 versions - Latest release: 2 months ago - 563 dependent packages - 11.4 million downloads total - 1 maintainer
IRanges 2.44.0
Foundation of integer range manipulation in Bioconductor8 versions - Latest release: 2 months ago - 563 dependent packages - 11.4 million downloads total - 1 maintainer
Top 1.7% on bioconductor.org
7 versions - Latest release: 2 months ago - 43 dependent packages - 1.14 million downloads total - 3 maintainers
sva 3.58.0
Surrogate Variable Analysis7 versions - Latest release: 2 months ago - 43 dependent packages - 1.14 million downloads total - 3 maintainers
Top 1.0% on bioconductor.org
7 versions - Latest release: 2 months ago - 45 dependent packages - 5.27 million downloads total - 1 maintainer
MatrixGenerics 1.22.0
S4 Generic Summary Statistic Functions that Operate on Matrix-Like Objects7 versions - Latest release: 2 months ago - 45 dependent packages - 5.27 million downloads total - 1 maintainer
RNAsense 1.24.0
Analysis of Time-Resolved RNA-Seq Data6 versions - Latest release: about 1 month ago - 9.76 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 0.1% on bioconductor.org
10 versions - Latest release: 26 days ago - 604 dependent packages - 9.08 million downloads total - 1 maintainer
GenomicRanges 1.62.1
Representation and manipulation of genomic intervals10 versions - Latest release: 26 days ago - 604 dependent packages - 9.08 million downloads total - 1 maintainer
Top 0.3% on bioconductor.org
16 versions - Latest release: 2 months ago - 322 dependent packages - 6.83 million downloads total - 1 maintainer
limma 3.66.0
Linear Models for Microarray and Omics Data16 versions - Latest release: 2 months ago - 322 dependent packages - 6.83 million downloads total - 1 maintainer
Top 2.0% on bioconductor.org
6 versions - Latest release: 2 months ago - 6 dependent packages - 311 thousand downloads total - 1 maintainer
ROC 1.86.0
utilities for ROC, with microarray focus6 versions - Latest release: 2 months ago - 6 dependent packages - 311 thousand downloads total - 1 maintainer
Top 1.4% on bioconductor.org
6 versions - Latest release: 2 months ago - 33 dependent packages - 1.88 million downloads total - 1 maintainer
RBGL 1.86.0
An interface to the BOOST graph library6 versions - Latest release: 2 months ago - 33 dependent packages - 1.88 million downloads total - 1 maintainer
Top 0.9% on bioconductor.org
7 versions - Latest release: 2 months ago - 48 dependent packages - 4.66 million downloads total - 1 maintainer
annotate 1.88.0
Annotation for microarrays7 versions - Latest release: 2 months ago - 48 dependent packages - 4.66 million downloads total - 1 maintainer
Top 1.2% on bioconductor.org
19 versions - Latest release: 20 days ago - 59 dependent packages - 2.31 million downloads total - 1 maintainer
clusterProfiler 4.18.4
A universal enrichment tool for interpreting omics data19 versions - Latest release: 20 days ago - 59 dependent packages - 2.31 million downloads total - 1 maintainer
Top 0.1% on bioconductor.org
6 versions - Latest release: 2 months ago - 518 dependent packages - 11 million downloads total - 1 maintainer
Biobase 2.70.0
Biobase: Base functions for Bioconductor6 versions - Latest release: 2 months ago - 518 dependent packages - 11 million downloads total - 1 maintainer
Top 0.2% on bioconductor.org
7 versions - Latest release: 2 months ago - 632 dependent packages - 7.5 million downloads total - 1 maintainer
SummarizedExperiment 1.40.0
A container (S4 class) for matrix-like assays7 versions - Latest release: 2 months ago - 632 dependent packages - 7.5 million downloads total - 1 maintainer
Top 1.1% on bioconductor.org
10 versions - Latest release: 2 months ago - 377 dependent packages - 8.53 million downloads total - 63 stars on GitHub - 1 maintainer
BiocParallel 1.44.0
Bioconductor facilities for parallel evaluation10 versions - Latest release: 2 months ago - 377 dependent packages - 8.53 million downloads total - 63 stars on GitHub - 1 maintainer
Top 1.5% on bioconductor.org
6 versions - Latest release: 2 months ago - 9 dependent packages - 327 thousand downloads total - 481 stars on GitHub - 1 maintainer
maftools 2.26.0 💰
Summarize, Analyze and Visualize MAF Files6 versions - Latest release: 2 months ago - 9 dependent packages - 327 thousand downloads total - 481 stars on GitHub - 1 maintainer
Top 1.3% on bioconductor.org
6 versions - Latest release: 2 months ago - 44 dependent packages - 1.94 million downloads total - 1 maintainer
impute 1.84.0
impute: Imputation for microarray data6 versions - Latest release: 2 months ago - 44 dependent packages - 1.94 million downloads total - 1 maintainer
Top 1.9% on bioconductor.org
20 versions - Latest release: about 1 month ago - 15 dependent packages - 2.14 million downloads total - 1 maintainer
enrichplot 1.30.4
Visualization of Functional Enrichment Result20 versions - Latest release: about 1 month ago - 15 dependent packages - 2.14 million downloads total - 1 maintainer
scPCA 1.24.0
Sparse Contrastive Principal Component Analysis6 versions - Latest release: 2 months ago - 13.7 thousand downloads total - 12 stars on GitHub - 1 maintainer
Top 1.6% on bioconductor.org
13 versions - Latest release: 2 months ago - 27 dependent packages - 2.13 million downloads total - 1 maintainer
DOSE 4.4.0
Disease Ontology Semantic and Enrichment analysis13 versions - Latest release: 2 months ago - 27 dependent packages - 2.13 million downloads total - 1 maintainer
Top 0.8% on bioconductor.org
8 versions - Latest release: 2 months ago - 51 dependent packages - 4.94 million downloads total - 1 maintainer
flowCore 2.22.0
flowCore: Basic structures for flow cytometry data8 versions - Latest release: 2 months ago - 51 dependent packages - 4.94 million downloads total - 1 maintainer
Top 0.5% on bioconductor.org
11 versions - Latest release: about 2 months ago - 146 dependent packages - 4.1 million downloads total - 330 stars on GitHub - 1 maintainer
DESeq2 1.50.2
Differential gene expression analysis based on the negative binomial distribution11 versions - Latest release: about 2 months ago - 146 dependent packages - 4.1 million downloads total - 330 stars on GitHub - 1 maintainer
Top 1.8% on bioconductor.org
6 versions - Latest release: 2 months ago - 15 dependent packages - 497 thousand downloads total - 4 stars on GitHub - 1 maintainer
seqLogo 1.76.0
Sequence logos for DNA sequence alignments6 versions - Latest release: 2 months ago - 15 dependent packages - 497 thousand downloads total - 4 stars on GitHub - 1 maintainer
Top 1.9% on bioconductor.org
8 versions - Latest release: 2 months ago - 30 dependent packages - 575 thousand downloads total - 123 stars on GitHub - 1 maintainer
MSnbase 2.36.0
Base Functions and Classes for Mass Spectrometry and Proteomics8 versions - Latest release: 2 months ago - 30 dependent packages - 575 thousand downloads total - 123 stars on GitHub - 1 maintainer
Top 0.6% on bioconductor.org
8 versions - Latest release: 2 months ago - 132 dependent packages - 4.82 million downloads total - 1 maintainer
GenomicAlignments 1.46.0
Representation and manipulation of short genomic alignments8 versions - Latest release: 2 months ago - 132 dependent packages - 4.82 million downloads total - 1 maintainer
Top 1.3% on bioconductor.org
7 versions - Latest release: 2 months ago - 36 dependent packages - 1.95 million downloads total - 1 maintainer
ShortRead 1.68.0
FASTQ input and manipulation7 versions - Latest release: 2 months ago - 36 dependent packages - 1.95 million downloads total - 1 maintainer
Top 1.0% on bioconductor.org
9 versions - Latest release: 2 months ago - 38 dependent packages - 2.17 million downloads total - 345 stars on GitHub - 1 maintainer
fgsea 1.36.0
Fast Gene Set Enrichment Analysis9 versions - Latest release: 2 months ago - 38 dependent packages - 2.17 million downloads total - 345 stars on GitHub - 1 maintainer
Top 0.4% on bioconductor.org
7 versions - Latest release: 11 days ago - 251 dependent packages - 5.04 million downloads total - 1 maintainer
rtracklayer 1.70.1
R interface to genome annotation files and the UCSC genome browser7 versions - Latest release: 11 days ago - 251 dependent packages - 5.04 million downloads total - 1 maintainer
affyILM 1.62.0
Linear Model of background subtraction and the Langmuir isotherm6 versions - Latest release: about 1 month ago - 39.4 thousand downloads total - 1 maintainer
Top 3.2% on bioconductor.org
7 versions - Latest release: about 1 month ago - 14 dependent packages - 313 thousand downloads total - 1 maintainer
DropletUtils 1.30.0
Utilities for Handling Single-Cell Droplet Data7 versions - Latest release: about 1 month ago - 14 dependent packages - 313 thousand downloads total - 1 maintainer
brendaDb 1.24.0
The BRENDA Enzyme Database6 versions - Latest release: about 1 month ago - 11.1 thousand downloads total - 2 stars on GitHub - 1 maintainer
POMA 1.20.0
Tools for Omics Data Analysis6 versions - Latest release: about 2 months ago - 1 dependent package - 14.5 thousand downloads total - 12 stars on GitHub - 1 maintainer
Top 2.4% on bioconductor.org
6 versions - Latest release: about 1 month ago - 2 dependent packages - 299 thousand downloads total - 1 maintainer
DiffBind 3.20.0
Differential Binding Analysis of ChIP-Seq Peak Data6 versions - Latest release: about 1 month ago - 2 dependent packages - 299 thousand downloads total - 1 maintainer
specL 1.44.0
specL - Prepare Peptide Spectrum Matches for Use in Targeted Proteomics6 versions - Latest release: about 1 month ago - 22.9 thousand downloads total - 1 maintainer
Top 0.5% on bioconductor.org
9 versions - Latest release: 2 months ago - 183 dependent packages - 4.22 million downloads total - 1 maintainer
GenomicFeatures 1.62.0
Query the gene models of a given organism/assembly9 versions - Latest release: 2 months ago - 183 dependent packages - 4.22 million downloads total - 1 maintainer
Top 1.7% on bioconductor.org
6 versions - Latest release: 2 months ago - 30 dependent packages - 1.15 million downloads total - 1 maintainer
vsn 3.78.0
Variance stabilization and calibration for microarray data6 versions - Latest release: 2 months ago - 30 dependent packages - 1.15 million downloads total - 1 maintainer
Top 1.8% on bioconductor.org
6 versions - Latest release: 2 months ago - 12 dependent packages - 432 thousand downloads total - 1 maintainer
oligoClasses 1.72.0
Classes for high-throughput arrays supported by oligo and crlmm6 versions - Latest release: 2 months ago - 12 dependent packages - 432 thousand downloads total - 1 maintainer
Top 1.4% on bioconductor.org
8 versions - Latest release: 2 months ago - 54 dependent packages - 1.67 million downloads total - 1 maintainer
HDF5Array 1.38.0
HDF5 datasets as array-like objects in R8 versions - Latest release: 2 months ago - 54 dependent packages - 1.67 million downloads total - 1 maintainer
Top 4.1% on bioconductor.org
6 versions - Latest release: about 1 month ago - 1 dependent package - 89.1 thousand downloads total - 1 maintainer
makecdfenv 1.86.0
CDF Environment Maker6 versions - Latest release: about 1 month ago - 1 dependent package - 89.1 thousand downloads total - 1 maintainer
Top 0.5% on bioconductor.org
8 versions - Latest release: 2 months ago - 111 dependent packages - 7.6 million downloads total - 1 maintainer
DelayedArray 0.36.0
A unified framework for working transparently with on-disk and in-memory array-like datasets8 versions - Latest release: 2 months ago - 111 dependent packages - 7.6 million downloads total - 1 maintainer
Top 3.3% on bioconductor.org
7 versions - Latest release: about 1 month ago - 6 dependent packages - 350 thousand downloads total - 1 maintainer
ChIPseeker 1.46.1
ChIPseeker for ChIP peak Annotation, Comparison, and Visualization7 versions - Latest release: about 1 month ago - 6 dependent packages - 350 thousand downloads total - 1 maintainer
BloodGen3Module 1.18.0
This R package for performing module repertoire analyses and generating fingerprint representations6 versions - Latest release: about 1 month ago - 10.5 thousand downloads total - 1 maintainer
XeniumIO 1.2.0
Import and represent Xenium data from the 10X Xenium Analyzer2 versions - Latest release: about 1 month ago - 2.38 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 1.2% on bioconductor.org
6 versions - Latest release: 2 months ago - 37 dependent packages - 2.59 million downloads total - 1 maintainer
multtest 2.66.0
Resampling-based multiple hypothesis testing6 versions - Latest release: 2 months ago - 37 dependent packages - 2.59 million downloads total - 1 maintainer
ExploreModelMatrix 1.22.0
Graphical Exploration of Design Matrices7 versions - Latest release: about 1 month ago - 18.6 thousand downloads total - 37 stars on GitHub - 1 maintainer
pram 1.26.0
Pooling RNA-seq datasets for assembling transcript models6 versions - Latest release: about 1 month ago - 10.9 thousand downloads total - 1 stars on GitHub - 1 maintainer
RNAmodR.RiboMethSeq 1.24.0
Detection of 2'-O methylations by RiboMethSeq6 versions - Latest release: about 1 month ago - 10.9 thousand downloads total - 1 stars on GitHub - 1 maintainer
adductomicsR 1.26.0
Processing of adductomic mass spectral datasets6 versions - Latest release: about 1 month ago - 15 thousand downloads total - 1 stars on GitHub - 1 maintainer
MGFR 1.35.0
Marker Gene Finder in RNA-seq data6 versions - Latest release: about 1 month ago - 1 dependent package - 16.4 thousand downloads total - 1 maintainer
Top 1.8% on bioconductor.org
8 versions - Latest release: 2 months ago - 14 dependent packages - 411 thousand downloads total - 2 maintainers
Rsubread 2.24.0
Mapping, quantification and variant analysis of sequencing data8 versions - Latest release: 2 months ago - 14 dependent packages - 411 thousand downloads total - 2 maintainers
Top 9.0% on bioconductor.org
6 versions - Latest release: about 1 month ago - 12 dependent packages - 579 thousand downloads total - 5 stars on GitHub - 1 maintainer
illuminaio 0.52.0
Parsing Illumina Microarray Output Files6 versions - Latest release: about 1 month ago - 12 dependent packages - 579 thousand downloads total - 5 stars on GitHub - 1 maintainer
Top 0.1% on bioconductor.org
9 versions - Latest release: 2 months ago - 740 dependent packages - 10.9 million downloads total - 1 maintainer
S4Vectors 0.48.0
Foundation of vector-like and list-like containers in Bioconductor9 versions - Latest release: 2 months ago - 740 dependent packages - 10.9 million downloads total - 1 maintainer
Top 5.1% on bioconductor.org
6 versions - Latest release: about 1 month ago - 1 dependent package - 53.7 thousand downloads total - 1 maintainer
ACME 2.66.0
Algorithms for Calculating Microarray Enrichment (ACME)6 versions - Latest release: about 1 month ago - 1 dependent package - 53.7 thousand downloads total - 1 maintainer
IVAS 2.30.0
Identification of genetic Variants affecting Alternative Splicing6 versions - Latest release: about 1 month ago - 1 dependent package - 21.2 thousand downloads total - 1 maintainer
Top 7.0% on bioconductor.org
6 versions - Latest release: about 1 month ago - 43.6 thousand downloads total - 1 maintainer
SCAN.UPC 2.52.0
Single-channel array normalization (SCAN) and Universal exPression Codes (UPC)6 versions - Latest release: about 1 month ago - 43.6 thousand downloads total - 1 maintainer
PathNet 1.50.0
An R package for pathway analysis using topological information6 versions - Latest release: about 1 month ago - 27.1 thousand downloads total - 1 maintainer
Top 6.7% on bioconductor.org
6 versions - Latest release: about 1 month ago - 7 dependent packages - 69.3 thousand downloads total - 7 stars on GitHub - 1 maintainer
GenomicInteractions 1.44.0
Utilities for handling genomic interaction data6 versions - Latest release: about 1 month ago - 7 dependent packages - 69.3 thousand downloads total - 7 stars on GitHub - 1 maintainer
Top 1.0% on bioconductor.org
8 versions - Latest release: 2 months ago - 201 dependent packages - 1.94 million downloads total - 1 maintainer
SingleCellExperiment 1.32.0
S4 Classes for Single Cell Data8 versions - Latest release: 2 months ago - 201 dependent packages - 1.94 million downloads total - 1 maintainer
FastqCleaner 1.28.0
A Shiny Application for Quality Control, Filtering and Trimming of FASTQ Files6 versions - Latest release: about 1 month ago - 16.2 thousand downloads total - 1 maintainer
fastreeR 2.0.0
Phylogenetic, Distance and Other Calculations on VCF and Fasta Files8 versions - Latest release: about 1 month ago - 8.57 thousand downloads total - 24 stars on GitHub - 1 maintainer
CompoundDb 1.14.0
Creating and Using (Chemical) Compound Annotation Databases7 versions - Latest release: about 1 month ago - 3 dependent packages - 28.2 thousand downloads total - 19 stars on GitHub - 1 maintainer
Top 9.0% on bioconductor.org
6 versions - Latest release: about 1 month ago - 34.7 thousand downloads total - 1 maintainer
maCorrPlot 1.80.0
Visualize artificial correlation in microarray data6 versions - Latest release: about 1 month ago - 34.7 thousand downloads total - 1 maintainer
Top 9.0% on bioconductor.org
6 versions - Latest release: about 1 month ago - 35.9 thousand downloads total - 1 maintainer
diffGeneAnalysis 1.92.0
Performs differential gene expression Analysis6 versions - Latest release: about 1 month ago - 35.9 thousand downloads total - 1 maintainer
zenith 1.12.0
Gene set analysis following differential expression using linear (mixed) modeling with dream7 versions - Latest release: about 1 month ago - 2 dependent packages - 11.1 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 5.8% on bioconductor.org
6 versions - Latest release: about 1 month ago - 3 dependent packages - 58.4 thousand downloads total - 1 maintainer
fabia 2.56.0
FABIA: Factor Analysis for Bicluster Acquisition6 versions - Latest release: about 1 month ago - 3 dependent packages - 58.4 thousand downloads total - 1 maintainer
GUIDEseq 1.40.0
GUIDE-seq and PEtag-seq analysis pipeline6 versions - Latest release: about 1 month ago - 1 dependent package - 21.8 thousand downloads total - 1 maintainer
Melissa 1.25.0
Bayesian clustering and imputationa of single cell methylomes6 versions - Latest release: about 1 month ago - 10.7 thousand downloads total - 1 maintainer
nipalsMCIA 1.8.0
Multiple Co-Inertia Analysis via the NIPALS Method9 versions - Latest release: about 2 months ago - 5.9 thousand downloads total - 7 stars on GitHub - 1 maintainer
Related Keywords
GeneExpression
664
Sequencing
659
Visualization
482
ImmunoOncology
460
RNASeq
438
DifferentialExpression
420
Microarray
375
DataImport
368
SingleCell
341
Clustering
320
Transcriptomics
297
Preprocessing
290
Infrastructure
269
QualityControl
255
Genetics
227
Proteomics
208
Transcription
199
Classification
195
MultipleComparison
194
Network
189
Normalization
189
StatisticalMethod
183
GeneSetEnrichment
179
Coverage
175
Pathways
168
DataRepresentation
167
Regression
157
MassSpectrometry
156
Annotation
156
GraphAndNetwork
151
r
130
bioconductor
127
Metabolomics
125
DNAMethylation
124
GeneRegulation
123
SystemsBiology
112
FunctionalGenomics
109
Alignment
107
Epigenetics
106
ChIPSeq
100
Bayesian
98
BiomedicalInformatics
96
SNP
96
DimensionReduction
94
GO
84
Spatial
80
BatchEffect
79
CopyNumberVariation
78
bioinformatics
75
FlowCytometry
73
CellBasedAssays
73
CellBiology
72
OneChannel
72
GUI
71
NetworkInference
69
FeatureExtraction
69
KEGG
69
DifferentialMethylation
67
TwoChannel
64
TimeCourse
61
Microbiome
60
PrincipalComponent
58
GenomeAnnotation
58
SequenceMatching
57
bioconductor-package
57
NetworkEnrichment
57
GeneTarget
56
AlternativeSplicing
55
WorkflowStep
47
GeneticVariability
47
Survival
47
MethylationArray
47
DNASeq
44
ReportWriting
44
rstats
43
GenomicVariation
43
WholeGenome
43
GenomeWideAssociation
41
Metagenomics
41
ShinyApps
41
MethylSeq
40
ThirdPartyClient
39
DifferentialSplicing
39
ATACSeq
39
VariantAnnotation
37
ExperimentalDesign
36
FunctionalPrediction
35
BiologicalQuestion
35
HiC
35
r-package
34
GenePrediction
31
Reactome
30
Technology
29
mRNAMicroarray
28
SomaticMutation
28
genomics
28
PeakDetection
27
CRISPR
26
mass-spectrometry
26
MotifAnnotation
25