A B C D E F G H I J K L M N O P R S T U V W X Y Z
affy | Methods for Affymetrix Oligonucleotide Arrays |
affyio | Tools for parsing Affymetrix data files |
airway | RangedSummarizedExperiment for RNA-Seq in airway smooth muscle cells, by Himes et al PLoS One 2014 |
annotate | Annotation for microarrays |
AnnotationDbi | Manipulation of SQLite-based annotations in Bioconductor |
AnnotationFilter | Facilities for Filtering Bioconductor Annotation Resources |
AnnotationHub | Client to access AnnotationHub resources |
apeglm | Approximate posterior estimation for GLM coefficients |
askpass | Safe Password Entry for R, Git, and SSH |
assertthat | Easy Pre and Post Assertions |
backports | Reimplementations of Functions Introduced Since R-3.0.0 |
base | The R Base Package |
base64enc | Tools for base64 encoding |
bbmle | Tools for General Maximum Likelihood Estimation |
bdsmatrix | Routines for Block Diagonal Symmetric Matrices |
beeswarm | The Bee Swarm Plot, an Alternative to Stripchart |
BH | Boost C++ Header Files |
Biobase | Biobase: Base functions for Bioconductor |
BiocFileCache | Manage Files Across Sessions |
BiocGenerics | S4 generic functions used in Bioconductor |
BiocManager | Access the Bioconductor Project Package Repository |
BiocParallel | Bioconductor facilities for parallel evaluation |
BiocVersion | Set the appropriate version of Bioconductor packages |
biomaRt | Interface to BioMart databases (i.e. Ensembl) |
Biostrings | Efficient manipulation of biological strings |
bit | Classes and Methods for Fast Memory-Efficient Boolean Selections |
bit64 | A S3 Class for Vectors of 64bit Integers |
bitops | Bitwise Operations |
blob | A Simple S3 Class for Representing Vectors of Binary Data ('BLOBS') |
broom | Convert Statistical Objects into Tidy Tibbles |
callr | Call R from R |
caTools | Tools: Moving Window Statistics, GIF, Base64, ROC AUC, etc |
cellranger | Translate Spreadsheet Cell Ranges to Rows and Columns |
cli | Helpers for Developing Command Line Interfaces |
clipr | Read and Write from the System Clipboard |
coda | Output Analysis and Diagnostics for MCMC |
colorspace | A Toolbox for Manipulating and Assessing Colors and Palettes |
commonmark | High Performance CommonMark and Github Markdown Rendering in R |
compiler | The R Compiler Package |
config | Manage Environment Specific Configuration Values |
crayon | Colored Terminal Output |
curl | A Modern and Flexible Web Client for R |
data.table | Extension of `data.frame` |
datasets | The R Datasets Package |
DBI | R Database Interface |
dbplyr | A 'dplyr' Back End for Databases |
DelayedArray | A unified framework for working transparently with on-disk and in-memory array-like datasets |
desc | Manipulate DESCRIPTION Files |
DESeq2 | Differential gene expression analysis based on the negative binomial distribution |
DEXSeq | Inference of differential exon usage in RNA-Seq |
digest | Create Compact Hash Digests of R Objects |
dplyr | A Grammar of Data Manipulation |
DRIMSeq | Differential transcript usage and tuQTL analyses with Dirichlet-multinomial model in RNA-seq |
edgeR | Empirical Analysis of Digital Gene Expression Data in R |
ellipsis | Tools for Working with ... |
emdbook | Support Functions and Data for "Ecological Models and Data" |
ensembldb | Utilities to create and use Ensembl-based annotation databases |
evaluate | Parsing and Evaluation Tools that Provide More Details than the Default |
fansi | ANSI Control Sequence Aware String Functions |
farver | High Performance Colour Space Manipulation |
fastmap | Fast Implementation of a Key-Value Store |
fastmatch | Fast match() function |
fgsea | Fast Gene Set Enrichment Analysis |
forcats | Tools for Working with Categorical Variables (Factors) |
formatR | Format R Code Automatically |
fs | Cross-Platform File System Operations Based on 'libuv' |
futile.logger | A Logging Utility for R |
futile.options | Futile Options Management |
genefilter | genefilter: methods for filtering genes from high-throughput experiments |
geneplotter | Graphics related functions for Bioconductor |
generics | Common S3 Generics not Provided by Base R Methods Related to Model Fitting |
GenomeInfoDb | Utilities for manipulating chromosome names, including modifying them to follow a particular naming style |
GenomeInfoDbData | Species and taxonomy ID look up tables used by GenomeInfoDb |
GenomicAlignments | Representation and manipulation of short genomic alignments |
GenomicFeatures | Conveniently import and query gene models |
GenomicRanges | Representation and manipulation of genomic intervals |
ggbeeswarm | Categorical Scatter (Violin Point) Plots |
ggplot2 | Create Elegant Data Visualisations Using the Grammar of Graphics |
ggrepel | Automatically Position Non-Overlapping Text Labels with 'ggplot2' |
ggvenn | Draw Venn Diagram by 'ggplot2' |
glmpca | Dimension Reduction of Non-Normally Distributed Data |
glue | Interpreted String Literals |
gplots | Various R Programming Tools for Plotting Data |
graphics | The R Graphics Package |
grDevices | The R Graphics Devices and Support for Colours and Fonts |
grid | The Grid Graphics Package |
gridExtra | Miscellaneous Functions for "Grid" Graphics |
gtable | Arrange 'Grobs' in Tables |
gtools | Various R Programming Tools |
haven | Import and Export 'SPSS', 'Stata' and 'SAS' Files |
hexbin | Hexagonal Binning Routines |
highr | Syntax Highlighting for R Source Code |
hms | Pretty Time of Day |
htmltools | Tools for HTML |
httpuv | HTTP and WebSocket Server Library |
httr | Tools for Working with URLs and HTTP |
hwriter | HTML Writer - Outputs R objects in HTML format |
interactiveDisplayBase | Base package for enabling powerful shiny web displays of Bioconductor objects |
IRanges | Foundation of integer range manipulation in Bioconductor |
isoband | Generate Isolines and Isobands from Regularly Spaced Elevation Grids |
jsonlite | A Robust, High Performance JSON Parser and Generator for R |
keras | R Interface to 'Keras' |
KernSmooth | Functions for Kernel Smoothing Supporting Wand & Jones (1995) |
knitr | A General-Purpose Package for Dynamic Report Generation in R |
labeling | Axis Labeling |
lambda.r | Modeling Data with Functional Programming |
later | Utilities for Scheduling Functions to Execute Later with Event Loops |
lattice | Trellis Graphics for R |
lazyeval | Lazy (Non-Standard) Evaluation |
lifecycle | Manage the Life Cycle of your Package Functions |
limma | Linear Models for Microarray Data |
locfit | Local Regression, Likelihood and Density Estimation |
lubridate | Make Dealing with Dates a Little Easier |
magrittr | A Forward-Pipe Operator for R |
markdown | Render Markdown with the C Library 'Sundown' |
MASS | Support Functions and Datasets for Venables and Ripley's MASS |
Matrix | Sparse and Dense Matrix Classes and Methods |
matrixStats | Functions that Apply to Rows and Columns of Matrices (and to Vectors) |
memoise | Memoisation of Functions |
methods | Formal Methods and Classes |
mgcv | Mixed GAM Computation Vehicle with Automatic Smoothness Estimation |
mime | Map Filenames to MIME Types |
modelr | Modelling Functions that Work with the Pipe |
msigdbr | MSigDB Gene Sets for Multiple Organisms in a Tidy Data Format |
munsell | Utilities for Using Munsell Colours |
mvtnorm | Multivariate Normal and t Distributions |
nlme | Linear and Nonlinear Mixed Effects Models |
numDeriv | Accurate Numerical Derivatives |
openssl | Toolkit for Encryption, Signatures and Certificates Based on OpenSSL |
org.Hs.eg.db | Genome wide annotation for Human |
parallel | Support for Parallel computation in R |
pheatmap | Pretty Heatmaps |
pillar | Coloured Formatting for Columns |
pkgbuild | Find Tools Needed to Build R Packages |
pkgconfig | Private Configuration for 'R' Packages |
pkgload | Simulate Package Installation and Attach |
plogr | The 'plog' C++ Logging Library |
plyr | Tools for Splitting, Applying and Combining Data |
praise | Praise Users |
preprocessCore | A collection of pre-processing functions |
prettyunits | Pretty, Human Readable Formatting of Quantities |
processx | Execute and Control System Processes |
progress | Terminal Progress Bars |
promises | Abstractions for Promise-Based Asynchronous Programming |
ProtGenerics | S4 generic functions for Bioconductor proteomics infrastructure |
ps | List, Query, Manipulate System Processes |
purrr | Functional Programming Tools |
R6 | Encapsulated Classes with Reference Semantics |
rappdirs | Application Directories: Determine Where to Save Data, Caches, and Logs |
RColorBrewer | ColorBrewer Palettes |
Rcpp | Seamless R and C++ Integration |
RcppArmadillo | 'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra Library |
RcppEigen | 'Rcpp' Integration for the 'Eigen' Templated Linear Algebra Library |
RcppNumerical | 'Rcpp' Integration for Numerical Computing Libraries |
RCurl | General Network (HTTP/FTP/...) Client Interface for R |
readr | Read Rectangular Text Data |
readxl | Read Excel Files |
rematch | Match Regular Expressions with a Nicer 'API' |
reprex | Prepare Reproducible Example Code via the Clipboard |
reshape2 | Flexibly Reshape Data: A Reboot of the Reshape Package |
reticulate | Interface to 'Python' |
Rhtslib | HTSlib high-throughput sequencing library as an R package |
rlang | Functions for Base Types and Core R and 'Tidyverse' Features |
rmarkdown | Dynamic Documents for R |
rprojroot | Finding Files in Project Subdirectories |
Rsamtools | Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import |
RSQLite | 'SQLite' Interface for R |
rstudioapi | Safely Access the RStudio API |
rtracklayer | R interface to genome annotation files and the UCSC genome browser |
rvest | Easily Harvest (Scrape) Web Pages |
S4Vectors | Foundation of vector-like and list-like containers in Bioconductor |
scales | Scale Functions for Visualization |
selectr | Translate CSS Selectors to XPath Expressions |
shiny | Web Application Framework for R |
snow | Simple Network of Workstations |
sourcetools | Tools for Reading, Tokenizing and Parsing R Code |
splines | Regression Spline Functions and Classes |
stageR | stageR: stage-wise analysis of high throughput gene expression data in R |
statmod | Statistical Modeling |
stats | The R Stats Package |
stats4 | Statistical Functions using S4 Classes |
stringi | Character String Processing Facilities |
stringr | Simple, Consistent Wrappers for Common String Operations |
SummarizedExperiment | SummarizedExperiment container |
survival | Survival Analysis |
sys | Powerful and Reliable Tools for Running System Commands in R |
tcltk | Tcl/Tk Interface |
tensorflow | R Interface to 'TensorFlow' |
testthat | Unit Testing for R |
tfruns | Training Run Tools for 'TensorFlow' |
tibble | Simple Data Frames |
tidyr | Tidy Messy Data |
tidyselect | Select from a Set of Strings |
tidyverse | Easily Install and Load the 'Tidyverse' |
tinytex | Helper Functions to Install and Maintain TeX Live, and Compile LaTeX Documents |
tools | Tools for Package Development |
tximeta | Transcript Quantification Import with Automatic Metadata |
tximport | Import and summarize transcript-level estimates for transcript- and gene-level analysis |
utf8 | Unicode Text Processing |
utils | The R Utils Package |
vctrs | Vector Helpers |
vipor | Plot Categorical Data Using Quasirandom Noise and Density Estimates |
viridisLite | Default Color Maps from 'matplotlib' (Lite Version) |
vsn | Variance stabilization and calibration for microarray data |
whisker | {{mustache}} for R, Logicless Templating |
withr | Run Code 'With' Temporarily Modified Global State |
xfun | Miscellaneous Functions by 'Yihui Xie' |
XML | Tools for Parsing and Generating XML Within R and S-Plus |
xml2 | Parse XML |
xtable | Export Tables to LaTeX or HTML |
XVector | Foundation of external vector representation and manipulation in Bioconductor |
yaml | Methods to Convert R Data to YAML and Back |
zeallot | Multiple, Unpacking, and Destructuring Assignment |
zlibbioc | An R packaged zlib-1.2.5 |