basilisk
basilisk: a Bioconductor package for managing Python environments - Published in JOSS (2022)
biotmle
biotmle: Targeted Learning for Biomarker Discovery - Published in JOSS (2017)
BASiCS
BASiCS: Bayesian Analysis of Single-Cell Sequencing Data. This is an unstable experimental version. Please see http://bioconductor.org/packages/BASiCS/ for the official release version
GeneTonic
Enjoy your transcriptomic data and analysis responsibly - like sipping a cocktail
GenomicSuperSignature
Interpretation of RNAseq experiments through robust, efficient comparison to public databases
raer
Characterize A-to-I RNA editing in bulk and single-cell RNA sequencing experiments
PureCN
Copy number calling and variant classification using targeted short read sequencing
https://github.com/ctriermaansson/dnafusion
Identification of gene-fusions, including EML4-ALK
mungesumstats
Rapid standardisation and quality control of GWAS or QTL summary statistics
cBioPortalData
Integrate the cancer genomics portal, cBioPortal, using MultiAssayExperiment
deconvR
The deconvR is an R package designed for analyzing deconvolution of the bulk sample(s) using an atlas of reference omic signature profiles and a user-selected model.
msPurity
A Bioconductor R package - Automated Evaluation of Precursor Ion Purity for Mass Spectrometry Based Fragmentation in Metabolomics
orthogene
🧬 o r t h o g e n e 🧬✨✨✨✨✨✨✨ Interspecies gene mapping✨✨✨✨✨ 🦠 🔁 🌱 🔁 🌳 🔁 🍎 🔁 🍊 🔁 🪱 🔁 🪰 🔁 🐟 🔁 🦎 🔁 🐓 🔁 🦇 🔁 🐄 🔁 🐖 🔁 🐐 🔁 🐎 🔁 🐈 🔁 🐕 🔁 🐁 🔁 🐒 🔁 🦧 🔁 🦍 🔁 🏃♀️
crisprDesign
Comprehensive design of CRISPR gRNAs for nucleases and base editors
HDTD
Characterization of intra-individual variability using physiologically relevant measurements provides important insights into fundamental biological questions ranging from cell type identity to tumor development. For each individual, the data measurements can be written as a matrix with the different subsamples of the individual recorded in the columns and the different phenotypic units recorded in the rows. Datasets of this type are called high-dimensional transposable data. The HDTD package provides functions for conducting statistical inference for the mean relationship between the row and column variables and for the covariance structure within and between the row and column variables.
https://github.com/bioconductor/biostrings
Efficient manipulation of biological strings
https://github.com/bioconductor/genomicranges
Representation and manipulation of genomic intervals
https://github.com/bioconductor/iranges
Foundation of integer range manipulation in Bioconductor
https://github.com/bioconductor/delayedarray
A unified framework for working transparently with on-disk and in-memory array-like datasets
SC3
A tool for the unsupervised clustering of cells from single cell RNA-Seq experiments
https://github.com/bioconductor/biobase
Biobase: Base functions for Bioconductor
https://github.com/bioconductor/organism.dplyr
BiocSingular
Clone of the Bioconductor repository for the BiocSingular package.
https://github.com/bioconductor/genomicfiles
Distributed computing by file or by range
https://github.com/bioconductor/gpls
Classification using generalized partial least squares
CopyNumberPlots
R package to create plots representing copy number data using karyoploteR
https://github.com/bioconductor/biocbaseutils
https://github.com/bioconductor/biocio
Standard input / output framework for use by Bioconductor packages
https://github.com/bioconductor/biocset
Representing Different Biological Sets
structToolbox
R/Bioconductor package - STRUCT (STatistics in R Using Class Templates) Toolbox: An extensive set of data (pre-)processing and analysis methods and tools for metabolomics and other omics,
pram
An R/Bioconductor package to predict intergenic transcript models from RNA-seq
https://github.com/bioconductor/gostats
Tools for manipulating GO and microarrays.
cellmigRation
An R package for tracking cells and analyzing their trajectories
https://github.com/bioconductor/cocitestats
Different test statistics based on co-citation.
BatchSVG
Identification of biased features from SVGs in spatial transcriptomics data
motifpeeker
Benchmark Epigenomic Profiling Methods with Motif Enrichment as Key Metric
https://github.com/bioconductor/organismdbi
Software to enable the smooth interfacing of different database packages
https://github.com/bioconductor/biocgenerics
Defines many S4 generic functions used in Bioconductor
singlecellmultimodal
Single Cell multimodal data scripts for downloading datasets
https://github.com/christinehou11/humanhippocampus2024
Access to spatial HPC project data
https://github.com/bioconductor/bsgenome
Software infrastructure for efficient representation of full genomes and their SNPs
https://github.com/bioconductor/rsamtools
Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import
https://github.com/bioconductor/ucsc.utils
Low-level utilities to retrieve data from the UCSC Genome Browser
https://github.com/bioconductor/s4arrays
Foundation of array-like containers in Bioconductor
https://github.com/bioconductor/hdf5array
HDF5 datasets as array-like objects in R
https://github.com/bioconductor/s4vectors
Foundation of vector-like and list-like containers in Bioconductor
https://github.com/bioconductor/annotationdbi
Manipulation of SQLite-based annotations in Bioconductor
https://github.com/bioconductor/summarizedexperiment
A container (S4 class) for matrix-like assays
https://github.com/bioconductor/matrixgenerics
S4 Generic Summary Statistic Functions that Operate on Matrix-Like Objects
https://github.com/bioconductor/ensemblvep
[DEPRECATED] R Interface to Ensembl Variant Effect Predictor
https://github.com/bioconductor/genefilter
genefilter: methods for filtering genes from high-throughput experiments
https://github.com/bioconductor/graph
graph: A package to handle graph data structures
https://github.com/bioconductor/bsgenomeforge
Forge your own BSgenome data package
https://github.com/bioconductor/hypergraph
A package providing hypergraph data structures
https://github.com/bioconductor/genomicfeatures
Query the gene models of a given organism/assembly
https://github.com/bioconductor/genemeta
MetaAnalysis for High Throughput Experiments
https://github.com/bioconductor/biocviews
Categorized views of R package repositories
https://github.com/bioconductor/variantannotation
Annotation of Genetic Variants
https://github.com/bioconductor/genomeinfodb
Utilities for manipulating chromosome names, including modifying them to follow a particular naming style
https://github.com/bioconductor/gseabase
Gene set enrichment data structures and methods
https://github.com/bioconductor/splicinggraphs
Create, manipulate, visualize splicing graphs, and assign RNA-seq reads to them
https://github.com/bioconductor/sparsearray
High-performance sparse data representation and manipulation in R
https://github.com/bioconductor/rhtslib
HTSlib high-throughput sequencing library as an R package
https://github.com/bioconductor/geneplotter
Graphics related functions for Bioconductor
https://github.com/bioconductor/experimenthubdata
Add resources to ExperimentHub
https://github.com/bioconductor/txdbmaker
A set of tools for making TxDb objects from genomic annotations from various sources (e.g. UCSC, Ensembl, and GFF files)
https://github.com/bioconductor/genomicalignments
Representation and manipulation of short genomic alignments