Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics - CRAN Task View

ACNE

Affymetrix SNP Probe-Summarization using Non-Negative Matrix Factoriza...

Version 0.9.1

ADAPTS

Automated Deconvolution Augmentation of Profiles for Tissue Specific C...

Version 1.0.22

alakazam

Immunoglobulin Clonal Lineage and Diversity Analysis

Version 1.3.0

aLFQ

Estimating Absolute Protein Quantities from Label-Free LC-MS/MS Proteo...

Version 1.3.6

aliases2entrez

Converts Human gene symbols to entrez IDs

Version 0.1.2

Allspice

RNA-Seq Profile Classifier

Version 1.0.7

AnaCoDa

Analysis of Codon Data under Stationarity using a Bayesian Framework

Version 0.1.4.4

AnnotationBustR

Extract Subsequences from GenBank Annotations

Version 1.3.0

BisqueRNA

Decomposition of Bulk Expression with Single-Cell Sequencing

Version 1.0.5

aroma.cn

Copy-Number Analysis of Large Microarray Data Sets

Version 1.7.1

bayefdr

Bayesian Estimation and Optimisation of Expected False Discovery Rate

Version 0.2.1

babelgene

Gene Orthologs for Model Organisms in a Tidy Data Format

Version 22.9

BarcodingR

Species Identification using DNA Barcodes

Version 1.0-3

BASiNET

Classification of RNA Sequences using Complex Network Theory

Version 0.0.5

biomartr

Genomic Data Retrieval

Version 1.0.7

BClustLonG

A Dirichlet Process Mixture Model for Clustering Longitudinal Gene Exp...

Version 0.1.3

DiscreteFDR

FDR Based Multiple Testing Procedures with Adaptation for Discrete Tes...

Version 2.0.0

BiasCorrector

A GUI to Correct Measurement Bias in DNA Methylation Analyses

Version 0.2.2

bio3d

Biological Structure Analysis

Version 2.4-4

BioInsight

Filter and Plot RNA Biotypes

Version 0.3.1

bioseq

A Toolbox for Manipulating Biological Sequences

Version 0.1.4

BRINDA

Computation of BRINDA Adjusted Micronutrient Biomarkers for Inflammati...

Version 0.1.5

CePa

Centrality-Based Pathway Enrichment

Version 0.8.0

CB2

CRISPR Pooled Screen Analysis using Beta-Binomial Test

Version 1.3.4

CeRNASeek

Identification and Analysis of ceRNA Regulation

Version 2.1.3

ChemoSpec

Exploratory Chemometrics for Spectroscopy

Version 6.1.10

chromoMap

Interactive Genomic Visualization of Biological Data

Version 4.1.1

clustermole

Unbiased Single-Cell Transcriptomic Data Cell Type Identification

Version 1.1.1

DGEobj.utils

Differential Gene Expression (DGE) Analysis Utility Toolkit

Version 1.0.6

compas

Conformational Manipulations of Protein Atomic Structures

Version 0.1.1

conos

Clustering on Network of Samples

Version 1.5.2

CovCombR

Combine Partial Covariance / Relationship Matrices

Version 1.0

cp4p

Calibration Plot for Proteomics

Version 0.3.6

cubfits

Codon Usage Bias Fits

Version 0.1-4

cumSeg

Change Point Detection in Genomic Sequences

Version 1.3

desiR

Desirability Functions for Ranking, Selecting, and Integrating Data

Version 1.2.2

depthTools

Depth Tools Package

Version 0.7

DGEobj

Differential Gene Expression (DGE) Analysis Results Data Object

Version 1.1.2

DiffCorr

Analyzing and Visualizing Differential Correlation Networks in Biologi...

Version 0.4.4

DiPALM

Differential Pattern Analysis via Linear Modeling

Version 1.2

directPA

Direction Analysis for Pathways and Kinases

Version 1.5.1

DIscBIO

A User-Friendly Pipeline for Biomarker Discovery in Single-Cell Transc...

Version 1.2.2

DRaWR

Discriminative Random Walk with Restart

Version 1.0.3

dynwrap

Representing and Inferring Single-Cell Trajectories

Version 1.2.4

DysPIA

Dysregulated Pathway Identification Analysis

Version 1.3

DysPIAData

Background and Pathway Data Used in 'DysPIA'

Version 0.1.2

func2vis

Clean and Visualize Over Expression Results from 'ConsensusPathDB'

Version 1.0-3

hommel

Methods for Closed Testing with Simes Inequality, in Particular Hommel...

Version 1.6

EMMIXgene

A Mixture Model-Based Approach to the Clustering of Microarray Express...

Version 0.1.4

enveomics.R

Various Utilities for Microbial Genomics and Metagenomics

Version 1.9.1

erah

Automated Spectral Deconvolution, Alignment, and Metabolite Identifica...

Version 2.0.1

PINSPlus

Clustering Algorithm for Data Integration and Disease Subtyping

Version 2.0.7

FiRE

Finder of Rare Entities (FiRE)

Version 1.0.1

flippant

Dithionite Scramblase Assay Analysis

Version 1.5.5

iq

Protein Quantification in Mass Spectrometry-Based Proteomics

Version 1.9.12

ftrCOOL

Feature Extraction from Biological Sequences

Version 2.0.0

GANPA

Gene Association Network-Based Pathway Analysis (GANPA)

Version 1.2

GANPAdata

The GANPA Datasets Package

Version 1.0

GeneCycle

Identification of Periodically Expressed Genes

Version 1.1.5

geneExpressionFromGEO

Easily Downloads a Gene Expression Dataset from a GEO Code and Retriev...

Version 0.9

GeneNet

Modeling and Inferring Gene Networks

Version 1.2.16

geno2proteo

Finding the DNA and Protein Sequences of Any Genomic or Proteomic Loci

Version 0.0.6

GenomicTools.fileHandler

File Handlers for Genomic Data Analysis

Version 0.1.5.9

genoPlotR

Plot Publication-Grade Gene and Genome Maps

Version 0.8.11

GOxploreR

Structural Exploration of the Gene Ontology (GO) Knowledge Base

Version 1.2.7

gprofiler2

Interface to the 'g:Profiler' Toolset

Version 0.2.3

prioGene

Candidate Gene Prioritization for Non-Communicable Diseases Based on F...

Version 1.0.1

GSA

Gene Set Analysis

Version 1.03.3

prioritylasso

Analyzing Multiple Omics Data with an Offset Approach

Version 0.3.1

RVA

RNAseq Visualization Automation

Version 0.0.5

iCARH

Integrative Conditional Autoregressive Horseshoe Model

Version 2.0.2.1

hsstan

Hierarchical Shrinkage Stan Models for Biomarker Selection

Version 0.8.2

HTSCluster

Clustering High-Throughput Transcriptome Sequencing (HTS) Data

Version 2.0.11

iCellR

Analyzing High-Throughput Single Cell Sequencing Data

Version 1.6.7

IMIX

Gaussian Mixture Model for Multi-Omics Data Integration

Version 1.1.5

immunarch

Bioinformatics Analysis of T-Cell and B-Cell Immune Repertoires

Version 0.9.1

imp4p

Imputation for Proteomics

Version 1.2

imputeLCMD

A Collection of Methods for Left-Censored Missing Data Imputation

Version 2.1

imsig

Immune Cell Gene Signatures for Profiling the Microenvironment of Soli...

Version 1.1.3

integIRTy

Integrating Multiple Modalities of High Throughput Assays Using Item R...

Version 1.0.7

InteRD

The Integrated and Robust Deconvolution

Version 0.1.1

ioncopy

Calling Copy Number Alterations in Amplicon Sequencing Data

Version 2.2.2

JBrowseR

An R Interface to the JBrowse 2 Genome Browser

Version 0.10.2

JSparO

Joint Sparse Optimization via Proximal Gradient Method for Cell Fate C...

Version 1.5.0

KRIS

Keen and Reliable Interface Subroutines for Bioinformatic Analysis

Version 1.1.6

krm

Kernel Based Regression Models

Version 2022.10-17

leapp

Latent Effect Adjustment After Primary Projection

Version 1.3

lilikoi

Metabolomics Personalized Pathway Analysis Tool

Version 2.1.1

lineup2

Lining Up Two Sets of Measurements

Version 0.6

lmQCM

An Algorithm for Gene Co-Expression Analysis

Version 0.2.4

LPS

Linear Predictor Score, for Binary Inference from Multiple Continuous ...

Version 1.0.16

LSPFP

Lysate and Secretome Peptide Feature Plotter

Version 1.0.3

MAAPER

Analysis of Alternative Polyadenylation Using 3' End-Linked Reads

Version 1.1.1

maGUI

A Graphical User Interface for Microarray Data Analysis and Annotation

Version 4.0

Map2NCBI

Mapping Markers to the Nearest Genomic Feature

Version 1.4

markerpen

Marker Gene Detection via Penalized Principal Component Analysis

Version 0.1.1

MCMC.qpcr

Bayesian Analysis of qRT-PCR Data

Version 1.2.4

metaboData

Example Metabolomics Data Sets

Version 0.6.3

MetabolicSurv

A Biomarker Validation Approach for Classification and Predicting Surv...

Version 1.1.2

MetabolomicsBasics

Basic Functions to Investigate Metabolomics Data Matrices

Version 1.4.5

metaMA

Meta-Analysis for MicroArrays

Version 3.1.3

metaRNASeq

Meta-Analysis of RNA-Seq Data

Version 1.0.7

MINTplates

Encode "License-Plates" from Sequences and Decode Them Back

Version 1.0.1

MiRNAQCD

Micro-RNA Quality Control and Diagnosis

Version 1.1.3

MOSS

Multi-Omic Integration via Sparse Singular Value Decomposition

Version 0.2.2

mpm

Multivariate Projection Methods

Version 1.0-23

mpmi

Mixed-Pair Mutual Information Estimators

Version 0.43.2.1

MetSizeR

A Shiny App for Sample Size Estimation in Metabolomic Experiments

Version 2.0.0

msigdbr

MSigDB Gene Sets for Multiple Organisms in a Tidy Data Format

Version 7.5.1

mutSignatures

Decipher Mutational Signatures from Somatic Mutational Catalogs

Version 2.1.1

tmod

Feature Set Enrichment Analysis for Metabolomics and Transcriptomics

Version 0.50.13

NBPSeq

Negative Binomial Models for RNA-Sequencing Data

Version 0.3.1

net4pg

Handle Ambiguity of Protein Identifications from Shotgun Proteomics

Version 0.1.1

netgsa

Network-Based Gene Set Analysis

Version 4.0.5

NewmanOmics

Extending the Newman Studentized Range Statistic to Transcriptomics

Version 1.0.11

driveR

Prioritizing Cancer Driver Genes Using Genomics Data

Version 0.4.1

omicwas

Cell-Type-Specific Association Testing in Bulk Omics Experiments

Version 0.8.0

omu

A Metabolomics Analysis Tool for Intuitive Figures and Convenient Meta...

Version 1.1.2

optBiomarker

Estimation of Optimal Number of Biomarkers for Two-Group Microarray Ba...

Version 1.0-28

OptCirClust

Circular, Periodic, or Framed Data Clustering: Fast, Optimal, and Repr...

Version 0.0.4

ORIClust

Order-Restricted Information Criterion-Based Clustering Algorithm

Version 1.0-2

packMBPLSDA

Multi-Block Partial Least Squares Discriminant Analysis

Version 0.9.0

pagoda2

Single Cell Analysis and Differential Expression

Version 1.0.12

pathfindR.data

Data Package for 'pathfindR'

Version 2.1.0

pathwayTMB

Pathway Based Tumor Mutational Burden

Version 0.1.3

pbm

Protein Binding Models

Version 1.2.1

PeakError

Compute the Label Error of Peak Calls

Version 2023.9.4

permPATH

Permutation Based Gene Expression Pathway Analysis

Version 1.3

pinfsc50

Sequence ('FASTA'), Annotation ('GFF') and Variants ('VCF') for 17 Sam...

Version 1.3.0

PSSMCOOL

Features Extracted from Position Specific Scoring Matrix (PSSM)

Version 0.2.4

PMA

Penalized Multivariate Analysis

Version 1.2-4

POD

Probability of Detection for Qualitative PCR Methods

Version 1.2.0

popPCR

Classify Digital PCR Droplets by Fitting Fluorescence Populations

Version 0.1.1.1

PQLseq

Efficient Mixed Model Analysis of Count Data in Large-Scale Genomic Se...

Version 1.2.1

PredCRG

Computational Prediction of Proteins Encoded by Circadian Genes

Version 1.0.2

SmCCNet

Sparse Multiple Canonical Correlation Network Analysis Tool

Version 2.0.3

Signac

Analysis of Single-Cell Chromatin Data

Version 1.14.0

PTXQC

Quality Report Generation for MaxQuant and mzTab Results

Version 1.1.1

slfm

Fitting a Bayesian Sparse Latent Factor Model in Gene Expression Analy...

Version 1.0.2

sccore

Core Utilities for Single-Cell RNA-Seq

Version 1.0.5

RNAseqNet

Log-Linear Poisson Graphical Model with Hot-Deck Multiple Imputation

Version 0.1.5

wrProteo

Proteomics Data Analysis Functions

Version 1.12.0

TCGAretriever

Retrieve Genomic and Clinical Data from CBioPortal Including TCGA Data

Version 1.9.1

singleCellHaystack

A Universal Differential Expression Prediction Tool for Single-Cell an...

Version 1.0.2

protViz

Visualizing and Analyzing Mass Spectrometry Related Data in Proteomics

Version 0.7.9

seqinr

Biological Sequences Retrieval and Analysis

Version 4.2-36

WGCNA

Weighted Correlation Network Analysis

Version 1.73

scTenifoldNet

Construct and Compare scGRN from Single-Cell Transcriptomic Data

Version 1.3

VAM

Variance-Adjusted Mahalanobis

Version 1.1.0

miic

Learning Causal or Non-Causal Graphical Models Using Information Theor...

Version 2.0.3

RAMClustR

Mass Spectrometry Metabolomics Feature Clustering and Interpretation

Version 1.3.1

scoper

Spectral Clustering-Based Method for Identifying B Cell Clones

Version 1.3.0

scINSIGHT

Interpretation of Heterogeneous Single-Cell Gene Expression Data

Version 0.1.4

SurrogateRegression

Surrogate Outcome Regression Analysis

Version 0.6.0.1

topologyGSA

Gene Set Analysis Exploiting Pathway Topology

Version 1.5.0

Tmisc

Turner Miscellaneous

Version 1.0.1

RHclust

Vector in Partition

Version 2.0.0

WebGestaltR

Gene Set Analysis Toolkit WebGestaltR

Version 0.4.6

volcano3D

3D Volcano Plots and Polar Plots for Three-Class Data

Version 2.0.9

Rediscover

Identify Mutually Exclusive Mutations

Version 0.3.2

RGBM

LS-TreeBoost and LAD-TreeBoost for Gene Regulatory Network Reconstruct...

Version 1.0-11

vhica

Vertical and Horizontal Inheritance Consistence Analysis

Version 0.2.8

toprdata

Gene and Exon Data from Ensembl

Version 1.0.2

SoupX

Single Cell mRNA Soup eXterminator

Version 1.6.2

RobustRankAggreg

Methods for Robust Rank Aggregation

Version 1.2.1

ICBioMark

Data-Driven Design of Targeted Gene Panels for Estimating Immunotherap...

Version 0.1.4

rBiasCorrection

Correct Bias in DNA Methylation Analyses

Version 0.3.4

ssize.fdr

Sample Size Calculations for Microarray Experiments

Version 1.3

whitening

Whitening and High-Dimensional Canonical Correlation Analysis

Version 1.4.0

SIBERG

Systematic Identification of Bimodally Expressed Genes Using RNAseq Da...

Version 2.0.3

TailRank

The Tail-Rank Statistic

Version 3.2.2

SIMMS

Subnetwork Integration for Multi-Modal Signatures

Version 1.3.2

RNentropy

Entropy Based Method for the Detection of Significant Variation in Gen...

Version 1.2.3

SMVar

Structural Model for Variances

Version 1.3.4

TcGSA

Time-Course Gene Set Analysis

Version 0.12.10

treefit

The First Software for Quantitative Trajectory Inference

Version 1.0.2

RCircos

Circos 2D Track Plot

Version 1.2.2

prozor

Minimal Protein Set Explaining Peptide Spectrum Matches

Version 0.3.1

sigora

Signature Overrepresentation Analysis

Version 3.1.1

ypssc

Yeast-Proteome Secondary-Structure Calculator

Version 1.1.0

SignacX

Cell Type Identification and Discovery from Single Cell Gene Expressio...

Version 2.2.5

supclust

Supervised Clustering of Predictor Variables Such as Genes

Version 1.1-1

sonicLength

Estimating Abundance of Clones from DNA Fragmentation Data

Version 1.4.7

read.gb

Open GenBank Files

Version 2.2

SeqNet

Generate RNA-Seq Data from Gene-Gene Association Networks

Version 1.1.3

SlaPMEG

Pathway Testing for Longitudinal Omics

Version 1.0.1

semmcmc

Bayesian Structural Equation Modeling in Multiple Omics Data Integrati...

Version 0.0.6

wilson

Web-Based Interactive Omics Visualization

Version 2.4.2

scSorter

Implementation of 'scSorter' Algorithm

Version 0.0.2

TCA

Tensor Composition Analysis

Version 1.2.1

scTenifoldKnk

In-Silico Knockout Experiments from Single-Cell Gene Regulatory Networ...

Version 1.0.1

RcmdrPlugin.depthTools

R Commander Depth Tools Plug-in

Version 1.4

scLink

Inferring Functional Gene Co-Expression Networks from Single Cell Data

Version 1.0.1

VALERIE

Visualising Splicing at Single-Cell Resolution

Version 1.1.0

scBio

Single Cell Genomics for Enhancing Cell Composition Inference from Bul...

Version 0.1.6

TGS

Rapid Reconstruction of Time-Varying Gene Regulatory Networks

Version 1.0.1

statVisual

Statistical Visualization Tools

Version 1.2.1

riceidconverter

Convert Biological ID from RAP or MSU to SYMBOL for Oryza Sativa

Version 1.1.1

RIdeogram

Drawing SVG Graphics to Visualize and Map Genome-Wide Data on Idiogram...

Version 0.2.2

adjclust

Adjacency-Constrained Clustering of a Block-Diagonal Similarity Matrix

Version 0.6.9

agvgd

An R Implementation of the 'Align-GVGD' Method

Version 0.1.2

ampir

Predict Antimicrobial Peptides

Version 1.1.0

oncoPredict

Drug Response Modeling and Biomarker Discovery

Version 1.2

ICAMS

In-Depth Characterization and Analysis of Mutational Signatures ('ICAM...

Version 2.3.12

interep

Interaction Analysis of Repeated Measure Data

Version 0.4.1

cbioportalR

Browse and Query Clinical and Genomic Data from cBioPortal

Version 1.1.0

hgnc

Download and Import the HUGO Gene Nomenclature Committee ('HGNC') Data...

Version 0.1.4

enrichR

Provides an R Interface to 'Enrichr'

Version 3.2

Cascade

Selection, Reverse-Engineering and Prediction in Cascade Networks

Version 2.1

glmmSeq

General Linear Mixed Models for Gene-Level Differential Expression

Version 0.5.5

diffEnrich

Given a List of Gene Symbols, Performs Differential Enrichment Analysi...

Version 0.1.2

ICDS

Identification of Cancer Dysfunctional Subpathway with Omics Data

Version 0.1.3

fbar

An Extensible Approach to Flux Balance Analysis

Version 0.6.0

valr

Genome Interval Arithmetic

Version 0.8.2

regnet

Network-Based Regularization for Generalized Linear Models

Version 1.0.1

PSCBS

Analysis of Parent-Specific DNA Copy Numbers

Version 0.67.0

NACHO

NanoString Quality Control Dashboard

Version 2.0.6

SMDIC

Identification of Somatic Mutation-Driven Immune Cells

Version 0.1.5

OmicNavigator

Open-Source Software for 'Omic' Data Analysis and Visualization

Version 1.13.13

tidyestimate

A Tidy Implementation of 'ESTIMATE'

Version 1.1.1

SCORPIUS

Inferring Developmental Chronologies from Single-Cell RNA Sequencing D...

Version 1.0.9

CascadeData

Experimental Data of Cascade Experiments in Genomics

Version 1.4

networkABC

Network Reverse Engineering with Approximate Bayesian Computation

Version 0.8-1

graphsim

Simulate Expression Data from 'igraph' Networks

Version 1.0.3

parmigene

Parallel Mutual Information Estimation for Gene Network Reconstruction

Version 1.1.0

rPanglaoDB

Download and Merge Single-Cell RNA-Seq Data from the PanglaoDB Databas...

Version 0.2.1

phateR

PHATE - Potential of Heat-Diffusion for Affinity-Based Transition Embe...

Version 1.0.7

MetaIntegrator

Meta-Analysis of Gene Expression Data

Version 2.1.3

gggenes

Draw Gene Arrow Maps in 'ggplot2'

Version 0.5.1

dsb

Normalize & Denoise Droplet Single Cell Protein Data (CITE-Seq)

Version 1.0.4

tinyarray

Expression Data Analysis and Visualization

Version 2.4.2

nanostringr

Performs Quality Control, Data Normalization, and Batch Effect Correct...

Version 0.4.2

rSEA

Simultaneous Enrichment Analysis

Version 2.1.2

BED

Biological Entity Dictionary (BED)

Version 1.5.2

ptm

Analyses of Protein Post-Translational Modifications

Version 1.0.1

seqgendiff

RNA-Seq Generation/Modification for Simulation

Version 1.2.4

sigminer

Extract, Analyze and Visualize Mutational Signatures for Genomic Varia...

Version 2.3.1

Seurat

Tools for Single Cell Genomics

Version 5.1.0

SeuratObject

Data Structures for Single Cell Data

Version 5.0.2

Patterns

Deciphering Biological Networks with Patterned Heterogeneous Measureme...

Version 1.5

pathfindR

Enrichment Analysis Utilizing Active Subnetworks

Version 2.4.1

DRomics

Dose Response for Omics

Version 2.6-0

PeakSegJoint

Joint Peak Detection in Several ChIP-Seq Samples

Version 2024.10.1

PeakSegDisk

Disk-Based Constrained Change-Point Detection

Version 2024.10.1

PeakSegOptimal

Optimal Segmentation Subject to Up-Down Constraints

Version 2024.10.1

mi4p

Multiple Imputation for Proteomics

Version 1.2

LUCIDus

LUCID with Multiple Omics Data

Version 3.0.3

lineup

Lining Up Two Sets of Measurements

Version 0.44

protti

Bottom-Up Proteomics and LiP-MS Quality Control and Data Analysis Tool...

Version 0.9.0

o2plsda

Multiomics Data Integration

Version 0.0.25

wrMisc

Analyze Experimental High-Throughput (Omics) Data

Version 1.15.2

ActivePathways

Integrative Pathway Enrichment Analysis of Multivariate Omics Data

Version 2.0.5

solvebio

The Official SolveBio API Client

Version 2.15.0

seeker

Simplified Fetching and Processing of Microarray and RNA-Seq Data

Version 1.1.6