Top Bioconductor Packages
- DESeq2: Differential gene expression analysis based on the negative binomial distribution.
- edgeR: Differential expression analysis of RNA-Seq and other count data.
- limma: Linear models for microarray data analysis.
- GenomicRanges: Representation and manipulation of genomic intervals and variables.
- SummarizedExperiment: Container for storing high-throughput assay data and metadata.
- SingleCellExperiment: Container for single-cell RNA-Seq data.
- AnnotationHub: Access to a variety of genome annotation resources.
- BiocGenerics: S4 generic functions used across Bioconductor packages.
- Rsamtools: Input/output, manipulation, and analysis of SAM/BAM files.
- biomaRt: Interface to BioMart databases like Ensembl.
- tximport: Import and summarize transcript-level estimates for gene-level analysis.
- VariantAnnotation: Annotation of variants detected by high-throughput sequencing.
- GenomicFeatures: Representation and manipulation of transcript annotation databases.
- Biostrings: Efficient manipulation of biological strings.
- Gviz: Plotting data and annotation information along genomic coordinates.
- ComplexHeatmap: Making complex, annotated heatmaps.
- scran: Methods for single-cell RNA-Seq data analysis.
- scater: Single-cell analysis tools for quality control, normalization, and visualization.
- IRanges: Infrastructure for representing and manipulating intervals.
- HDF5Array: HDF5 backend for DelayedArray objects.
- TCGAbiolinks: Tools for downloading, preparing, and analyzing TCGA data.
- edgeRun: High-performance differential expression analysis for RNA-Seq data.
- ChIPseeker: Annotation of peaks in ChIP-Seq data.
- clusterProfiler: Statistical analysis and visualization of functional profiles for genes and gene clusters.
- ensembldb: Utilities for working with Ensembl-based annotations.
- GEOquery: Get data from NCBI Gene Expression Omnibus (GEO).
- pathview: Pathway-based data integration and visualization.
- GSEABase: Gene set enrichment data structures and methods.
- GOstats: Tools for manipulating GO and microarray data.
- GO.db: A set of annotation maps describing the entire Gene Ontology.
- WGCNA: Weighted correlation network analysis for gene expression data.
- maftools: Analysis and visualization of mutation annotation format (MAF) files.
- DiffBind: Differential binding analysis of ChIP-Seq peak data.
- BSgenome: Infrastructure for Biostrings-based genome data packages.
- Rhtslib: High-throughput sequencing library as used by Rsamtools.
- ShortRead: Import and analyze high-throughput sequencing data.
- BiocParallel: Bioconductor facilities for parallel evaluation.
- msigdb: Import Molecular Signatures Database (MSigDB) gene sets.
- goseq: Gene Ontology analysis for RNA-Seq data.
- ReactomePA: Pathway enrichment analysis with Reactome Pathway Database.
- IRanges: Infrastructure for manipulating intervals on sequences.
- sva: Surrogate variable analysis for removing batch effects and other unwanted variation in high-throughput experiments.
- AnnotationForge: Tools for building SQLite-based annotation data packages.
- BioCycData: Access to BioCyc Pathway/Genome Database Collection.
- biovizBase: Basic graphic utilities for visualization of genomic data.
- scRNAseq: Single-cell RNA sequencing data package.
- TxDb.Hsapiens.UCSC.hg38.knownGene: Annotation package for TxDb object(s).
- SummarizedExperiment: Container for storing high-throughput assay data and metadata.
- GenomicAlignments: Representation and manipulation of short genomic alignments.
- rtracklayer: Extensible framework for interacting with multiple genome browsers.
Top General R Packages
- ggplot2: Data visualization package based on the Grammar of Graphics.
- dplyr: Data manipulation functions that simplify complex operations on data frames.
- tidyr: Tools for converting data to tidy format.
- stringr: Simple, consistent functions to manipulate strings.
- lubridate: Functions to work with date-times and timespans.
- shiny: Web application framework for R.
- caret: Classification and regression training package.
- rmarkdown: Dynamic documents for R.
- knitr: A general-purpose literate programming engine.
- data.table: Extension of data.frame for fast manipulation of large datasets.
- xtable: Export tables to LaTeX or HTML.
- forecast: Tools for forecasting and time series analysis.
- randomForest: Classification and regression based on a forest of trees using random inputs.
- survival: Survival analysis, including penalized likelihood.
- glmnet: Lasso and elastic-net regularized generalized linear models.
- plotly: Interactive, web-based graphs via plotly's JavaScript graphing library.
- sf: Simple features for R, for handling vector data.
- zoo: S3 infrastructure for regular and irregular time series.
- tm: Text mining package for text mining applications.
- lme4: Linear mixed-effects models using 'Eigen' and S4.
- httr: Tools for working with URLs and HTTP.
- rcpp: Seamless R and C++ integration.
- sp: Classes and methods for spatial data.
- leaflet: Create interactive web maps with the JavaScript 'Leaflet' library.
- MASS: Functions and datasets to support Venables and Ripley's MASS book.
- readr: Read rectangular data (csv, tsv, fwf).
- magrittr: Provides a mechanism for chaining commands with a new forward-pipe operator.
- haven: Import and export 'SPSS', 'Stata' and 'SAS' files.
- tibble: Modern re-imagining of data frames.
- purrr: Functional programming tools.
- janitor: Simple tools for examining and cleaning dirty data.
- forcats: Tools for working with categorical variables (factors).
- sparklyr: R interface for Apache Spark.
- odbc: Connect to ODBC compatible databases.
- curl: A Modern and Flexible Web Client for R.
- jsonlite: A Simple and Robust JSON Parser and Generator for R.
- xml2: A modern XML package.
- RCurl: General network (HTTP/FTP/...) client interface for R.
- highcharter: A wrapper for the 'Highcharts' library.
- DT: A wrapper of the DataTables JavaScript library.
- shiny: Easy interactive web applications with R.
- flexdashboard: R Markdown Format for Flexible Dashboards.
- DiagrammeR: Create graph diagrams and flowcharts using R.
- visNetwork: Network visualization using vis.js library.
- sf: Simple features for R.
- tmap: Thematic maps.
- mapview: Interactive viewing of spatial data.
- plotly: Create interactive web graphics via 'plotly.js'.
- dygraphs: Interface to 'dygraphs' JavaScript Charting Library.
- threejs: Interactive 3D scatter plots and globes.
This extended list provides a comprehensive overview of the most widely used Bioconductor and general R packages essential for bioinformatics, data analysis, and visualization. For more detailed information and exploration of these packages, you can visit the Bioconductor website and CRAN.