Biocview "ImmunoOncology"

A/B compartment inference from ATAC-seq and methylation array data
Accurate, high-resolution sample inference from amplicon sequencing data
Accurate, high-resolution sample inference from amplicon sequencing data
A collection of tools for imaging MS data processing
A correlation-based method for quality filtering of single-cell RNAseq data
Add-on to CellNOptR: Discretized time treatments
Add-on to DESeq to improve p-values and q-values
A DNA methylation classifier tool for the identification of pediatric brain tumor subtypes
A Framework for Quality Control
A Framework for Quality Control
A GAM based framework for analysis of ChIP-Seq data
A GAM based framework for analysis of ChIP-Seq data
A GatingML Interface for Cross Platform Cytometry Data Sharing
A GatingML Interface for Cross Platform Cytometry Data Sharing
AIMS : Absolute Assignment of Breast Cancer Intrinsic Molecular Subtype
A mass spectrometry imaging toolbox for statistical analysis
A model for network-based prioritisation of genes
Analysis and quantitation of isobarically tagged MSMS proteomics data
Analysis for short time-series data
Analysis for short time-series data
Analysis for short time-series data
Analysis of alternative splicing using RNA-Seq
Analysis of cell-based screens - revised version of cellHTS
Analysis of Copy Number Variation in Single-Cell-Sequencing Data
Analysis of Copy Number Variation in Single-Cell-Sequencing Data
Analysis Of Differential Abundance Taking Sample Variation Into Account
Analysis Of Differential Abundance Taking Sample Variation Into Account
Analysis of high-throughput microscopy-based screens
Analysis of Metabolomics GC/MS Data
Analytical R tools for Mass Spectrometry
Analytical R tools for Mass Spectrometry
Analytical R tools for Mass Spectrometry
Analytical Tools for MassArray Data
Analyze flow cytometric data using gate information
Analyze flow cytometric data using histogram information
Analyze Illumina Infinium DNA methylation arrays
Analyze Illumina Infinium DNA methylation arrays
Analyze Illumina Infinium DNA methylation arrays
Analyze isomiRs and miRNAs from small RNA-seq
Analyze isomiRs and miRNAs from small RNA-seq
Analyze thermal proteome profiling (TPP) experiments
Analyze thermal proteome profiling (TPP) experiments
Analyze Transcription Factor Enrichment
Analyze Transcription Factor Enrichment
An Easy-to-use Systematic pipeline for ATACseq data analysis
An Easy-to-use Systematic pipeline for ATACseq data analysis
An Easy-to-use Systematic pipeline for ATACseq data analysis
An Easy-to-use Systematic pipeline for ATACseq data analysis
An Easy-to-use Systematic pipeline for ATACseq data analysis
An effective identification of alternative splicing events using junction arrays and RNA-Seq data
An effective identification of alternative splicing events using junction arrays and RNA-Seq data
An Integrative Tool for ChIP- And RNA-Seq Based Primary Transcripts Detection and Quantification
An interactive tool for visualizing NGS signals and sequence motif densities along genomic features using average plots and heatmaps
An interactive tool for visualizing NGS signals and sequence motif densities along genomic features using average plots and heatmaps
An interface between R and MS-GF+
An interface package for the BIOM file format
An mzIdentML parser for R
An mzIdentML parser for R
Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach
Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach
Annotation and analysis of biological dynamical systems using flow cytometry
Annotation and analysis of biological dynamical systems using flow cytometry
A Normalization and Copy Number Variation Detection Method for Whole Exome Sequencing
An package for identification of novel peptides by customized database derived from RNA-Seq
An package for identification of novel peptides by customized database derived from RNA-Seq
An package for identification of novel peptides by customized database derived from RNA-Seq
An R interface for computational modeling of tumor progression
An R interface for computational modeling of tumor progression
An R interface to the Ontology Lookup Service
An R interface to the Ontology Lookup Service
An R package for flow data clustering
An R package for gene and isoform differential expression analysis of RNA-seq data
An R package for prediction of nucleosome positions
An R package for proteomics data quality control
An R package for quantitative integration and analysis of multiple omics assays from heterogeneous samples
An R package for quantitative integration and analysis of multiple omics assays from heterogeneous samples
An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms
An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms
An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms
An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms.
An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms.
An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms.
An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms.
An R package for the creation of complex genomic profile plots
An R package for the creation of complex genomic profile plots
An R Package for Unbiased Splicing Pathway Analysis
An R package to detect chromatin state switches from epigenomic data
An R package to detect chromatin state switches from epigenomic data
An R package to detect chromatin state switches from epigenomic data
A package for the analysis of GC-MS metabolite profiling data
A package for the analysis of GC-MS metabolite profiling data
A package for variant peptides detection and visualization in shotgun proteomics.
A package to run mixture models for truncated metabolomics data with normal or lognormal distributions
Approximate posterior estimation for GLM coefficients
Approximate posterior estimation for GLM coefficients
ArrayExpress High Throughput Sequencing Processing Pipeline
A search tool for single cell RNA-seq data by gene lists
A shiny GUI for MSGFplus
A small RNA-seq visualizer and analysis toolkit
Assess Differential Gene Expression Experiments with ERCC Controls
Assess Differential Gene Expression Experiments with ERCC Controls
Assessment of duplication rates in RNA-Seq datasets
Assessment of duplication rates in RNA-Seq datasets
Assign Properties to TNBC Patients
A suite of functions to facilitate zFPKM transformations
A suite of functions to facilitate zFPKM transformations
ATAC-seq Quality Control
ATAC-seq Quality Control
A tool for unsupervised projection of single cell RNA-seq data
A tool for unsupervised projection of single cell RNA-seq data
A toolkit for performing KNN-based statistics for flow and mass cytometry data
A toolkit for single-cell immune receptor profiling
a tool to perform statistical analysis of differential protein expression for quantitative proteomics data.
a tool to perform statistical analysis of differential protein expression for quantitative proteomics data.
A tool to use GO Subtrees to Tag and Annotate Genes within a set
A tool to use GO Subtrees to Tag and Annotate Genes within a set
A unifying bioinformatics framework for spatial proteomics
A unifying bioinformatics framework for spatial proteomics
Automated analysis of CRISPR experiments
Automated analysis of CRISPR experiments
Automated Optimization of XCMS Data Processing parameters
Automated Quadratic Characterization of Flow Cytometer Instrument Sensitivity: Q, B and CV instrinsic calculations
Automatic and interactive quality control for flow cytometry data
Automatic and interactive quality control for flow cytometry data
Automatic and interactive quality control for flow cytometry data
Baffling Recursive Algorithm for Isotope distributioN calculations
Base Functions and Classes for Mass Spectrometry and Proteomics
Base Functions and Classes for Mass Spectrometry and Proteomics
Basic4Cseq: an R/Bioconductor package for analyzing 4C-seq data
Batch Effects Quality Control Software
Bayesian analysis for identifying gene or isoform expression changes in ordered RNA-seq experiments
Bayesian ANalysis Of Compositional Covariance
Bayesian Analysis of Differential Expression in RNA Sequencing Data
Bayesian Analysis of Single-Cell Sequencing data
Bayesian Analysis of Single-Cell Sequencing data
Bayesian clustering and imputationa of single cell methylomes
Bayesian clustering and imputationa of single cell methylomes
Bayesian hierarchical mixture of factor analyzers for modelling genomic bifurcations
bcbio Single-Cell RNA-Seq
bcbio Single-Cell RNA-Seq
BEARscc (Bayesian ERCC Assesstment of Robustness of Single Cell Clusters)
BEAT - BS-Seq Epimutation Analysis Toolkit
Better prediction by use of co-data: Adaptive group-regularized ridge regression
Better prediction by use of co-data: Adaptive group-regularized ridge regression
Bias Awared Peak Calling and Quantification for MeRIP-Seq
Bias Awared Peak Calling and Quantification for MeRIP-Seq
Bias Awared Peak Calling and Quantification for MeRIP-Seq
Bias-free Footprint Enrichment Test
Binomial test for Hi-C data analysis
Binomial test for Hi-C data analysis
Bioconductor components for general cancer genomics
Bioconductor components for general cancer genomics
Bioinformatics pipelines based on Rcwl
Bioinformatics pipelines based on Rcwl
Biological Network Analysis
Biological Network Analysis
Breakpoint analysis of time-course expression data
Breakpoint analysis of time-course expression data
Bump Hunter
Bump Hunter
Bump Hunter
Calculate growth-rate inhibition (GR) metrics
Calculate growth-rate inhibition (GR) metrics
Calculate strandness information of a bam file
Calculate strandness information of a bam file
Calculate strandness information of a bam file
Cancer Clone Finder
Cancer Clone Finder
Causal network analysis methods
ccrepe_and_nc.score
Cell OrderiNg by FluorEScence Signal
Characterization of Alternative Splicing based on Paired-End Reads
ChIP-Seq data scaling according to spike-in control
ChIP-Seq data scaling according to spike-in control
chroGPS2: Generation, visualization and differential analysis of epigenome maps
Chromatin Variation Across Regions
Chromatin Variation Across Regions
C++ infrastructure for representing and interacting with the gated cytometry
Ciphergen SELDI-TOF Processing
Clustering and Visualizing RNA-Seq Expression Data using Grade of Membership Models
Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq
Clustering for Flow Cytometry
Clustering for Flow Cytometry
Clustering of Time Series Gene Expression data
Cluster Merging for Flow Cytometry Data
Codon Usage Analysis and Prediction of Gene Expressivity
Codon Usage Analysis and Prediction of Gene Expressivity
Co-Expression Analysis of Sequencing Data
Co-Expression Analysis of Sequencing Data
Coexpression for Transcription Factors using Regulatory Impact Factors and Partial Correlation and Information Theory analysis
Coexpression for Transcription Factors using Regulatory Impact Factors and Partial Correlation and Information Theory analysis
Coexpression for Transcription Factors using Regulatory Impact Factors and Partial Correlation and Information Theory analysis
Coexpression for Transcription Factors using Regulatory Impact Factors and Partial Correlation and Information Theory analysis
Co-expression Modules identification Tool
Co-expression Modules identification Tool
Collection of annotation related methods for mass spectrometry data
Collection of annotation related methods for mass spectrometry data
Combinatorial and Differential Chromatin State Analysis for ChIP-Seq Data
Combinatorial and Differential Chromatin State Analysis for ChIP-Seq Data
Combinatorial Polyfunctionality Analysis of Single Cells
Combinatorial Polyfunctionality Analysis of Single Cells
Combines WGCNA and xCell readouts with bayesian network learrning to generate a Gene-Module Immune-Cell network (GMIC)
Combines WGCNA and xCell readouts with bayesian network learrning to generate a Gene-Module Immune-Cell network (GMIC)
Combining multitube flow cytometry data by binning
Compare Characteristic Features of Count Data Sets
Compare Characteristic Features of Count Data Sets
Computational pipeline for computing probability of modification from structure probing experiment data
Computational pipeline for computing probability of modification from structure probing experiment data
Computes estimates of the probability of related individuals sharing a rare variant
Conditional quantile normalization
Condition Comparison in scRNA-seq Data
Controlling bias and inflation in association studies using the empirical null distribution
Coordinate Covariation Analysis
Coordinate Covariation Analysis
Coordinate Covariation Analysis
Coordinated Gene Activity in Pattern Sets
Coordinated Gene Activity in Pattern Sets
Copy number calling and SNV classification using targeted short read sequencing
Copy number calling and SNV classification using targeted short read sequencing
Copy number information from targeted sequencing using off-target reads
Correction for natural isotope abundance and tracer purity in MS and MS/MS data from stable isotope labeling experiments
Correction for natural isotope abundance and tracer purity in MS and MS/MS data from stable isotope labeling experiments
cosmiq - COmbining Single Masses Into Quantities
cosmiq - COmbining Single Masses Into Quantities
Count summarization and normalization for RNA-Seq data
Covariate Assisted Large-scale Multiple testing
Covariate Assisted Large-scale Multiple testing
Coverage visualization package for R
Create, manipulate, visualize splicing graphs, and assign RNA-seq reads to them
Create, manipulate, visualize splicing graphs, and assign RNA-seq reads to them
Create rapid visualizations of RNAseq data in R
Create rapid visualizations of RNAseq data in R
Create rapid visualizations of RNAseq data in R
Cross omic genetic fingerprinting
Cross omic genetic fingerprinting
Cross-target analysis of small molecule bioactivity
Cytometry dATa anALYSis Tools
Cytometry dATa anALYSis Tools
Data analysis for cell-based functional assays
Data and code resources for microsatellite instability studies
Data extraction pipeline for large-scale GC-MS metabolomics datasets
Data Mining for RNA-seq data: normalization, feature selection and classification
Data Mining for RNA-seq data: normalization, feature selection and classification
Data preprocessing and quality control for Illumina HumanMethylation450 and MethylationEPIC BeadChip
Data preprocessing and quality control for Illumina HumanMethylation450 and MethylationEPIC BeadChip
Data preprocessing and quality control for Illumina HumanMethylation450 and MethylationEPIC BeadChip (USC version)
Decomposition of Isotopic Patterns
Decomposition of Isotopic Patterns
DeepBlueR
DeepBlueR
DeepBlueR
DegNorm: degradation normalization for RNA-seq data
derfinder helper package
derfinder helper package
Design of target-specific guide RNAs in CRISPR-Cas9, genome-editing systems
DEsingle for detecting three types of differential expression in single-cell RNA-seq data
DEsingle for detecting three types of differential expression in single-cell RNA-seq data
DEsubs: an R package for flexible identification of differentially expressed subpathways using RNA-seq expression experiments
Detect differential expression in microarray and proteomics datasets with the Power Law Global Error Model (PLGEM)
Detection and inference of differentially methylated regions from Whole Genome Bisulfite Sequencing
Detection and inference of differentially methylated regions from Whole Genome Bisulfite Sequencing
Determination of essential phenotypic elements of clusters in high-dimensional entities
Determination of essential phenotypic elements of clusters in high-dimensional entities
DEXUS - Identifying Differential Expression in RNA-Seq Studies with Unknown Conditions or without Replicates
Differential Abundant Analysis for Metabolomics and Proteomics Data
Differential Co-expression Analysis
Differential Co-expression Analysis
Differential discovery in high-dimensional cytometry via high-resolution clustering
Differential discovery in high-dimensional cytometry via high-resolution clustering
Differential Enrichment analysis of Proteomics data
Differential Enrichment analysis of Proteomics data
Differential Enrichment Scan 2
Differential Enrichment Scan 2
Differential expression analysis and model fitting for single-cell RNA-seq data
Differential expression analysis and model fitting for single-cell RNA-seq data
Differential Expression Analysis for RNA-seq data through a robust variance component test
Differential expression analysis of longitudinal count data sets
Differential expression analysis of longitudinal count data sets
Differential gene expression analysis based on the negative binomial distribution
Differential gene expression analysis based on the negative binomial distribution
Differential gene expression analysis based on the negative binomial distribution
Differential gene expression data formats converter
Differential transcript usage and tuQTL analyses with Dirichlet-multinomial model in RNA-seq
Differential transcript usage and tuQTL analyses with Dirichlet-multinomial model in RNA-seq
Dirichlet-Multinomial Mixture Model Machine Learning for Microbiome Data
Distance-correlation based Gene Set Analysis for longitudinal gene expression profiles
ELBOW - Evaluating foLd change By the lOgit Way
Empirical Analysis of Digital Gene Expression Data in R
Empirical Bayes estimate of block diagonal covariance matrices
Empirical RNA-seq Sample Size Analysis
Empirical RNA-seq Sample Size Analysis
Engineering Evaluation by Gene Categorization (eegc)
Engineering Evaluation by Gene Categorization (eegc)
Ensemble of Gene Set Enrichment Analyses
Epigenetic Dissection of Intra-Sample-Heterogeneity
Epigenetic Dissection of Intra-Sample-Heterogeneity
Estimate Pairwise Interactions from multidimensional features
Estimate proliferation in cell-tracking dye studies
Estimate protein complex membership using AP-MS protein data
ExCluster robustly detects differentially expressed exons between two conditions of RNA-seq data, requiring at least two independent biological replicates per condition
Experimental Design in Differential Abundance analysis
Exploration of marker-gene sequence taxonomic annotations
Exploration of marker-gene sequence taxonomic annotations
Exploratory analysis and differential expression for RNA-seq data
Exploratory Data Analysis and Normalization for RNA-Seq
Exploratory Data Analysis and Normalization for RNA-Seq
Exploratory Data Analysis of LC-MS/MS data by spectral counts
Explore and download data from the recount project
Explore and download data from the recount project
Exposome and omic data associatin and integration analysis
Factorial Latent Variable Modeling of Single-Cell RNA-Seq Data
Fast Correlation Based Filter for Feature Selection
Fast Correlation Based Filter for Feature Selection
Fast Sequence Mapping in High-Throughput shRNA and CRISPR Screens
FCBF-based Co-Expression Networks for Single Cells
FCBF-based Co-Expression Networks for Single Cells
FCBF-based Co-Expression Networks for Single Cells
Filter replicated high-throughput transcriptome sequencing data
Filter replicated high-throughput transcriptome sequencing data
Finding differentially expressed unannotated genomic regions from RNA-seq data
Finding differentially expressed unannotated genomic regions from RNA-seq data
Fingerprinting for Flow Cytometry
Fitting cell population growth models
Flexible, isoform-level differential expression analysis
flowBeads: Analysis of flow bead data
flowClean
flowClean
flowCore: Basic structures for flow cytometry data
flowCore: Basic structures for flow cytometry data
flowPlots: analysis plots and data class for gated flow cytometry data
FlowRepository R Interface
Functions to conduct quality control analysis in methylation data
Functions to conduct quality control analysis in methylation data
GaGa hierarchical model for high-throughput data analysis
GC-SIM-MS data processing and alaysis tool
GDCRNATools: an R/Bioconductor package for integrative analysis of lncRNA, mRNA, and miRNA data in GDC
GDCRNATools: an R/Bioconductor package for integrative analysis of lncRNA, mRNA, and miRNA data in GDC
Gene Ontology analyser for RNA-seq and other length biased data
Gene Ontology analyser for RNA-seq and other length biased data
Generally Applicable Gene-set Enrichment for Pathway Analysis
Generally applicable transcriptome-wide analysis of translational efficiency using anota2seq
General Sample Size and Power Analysis for Microarray and Next-Generation Sequencing Data
Generate customized protein database from NGS data, with a focus on RNA-Seq data, for proteomics search
Generate HTML or PDF reports for a set of genomic regions or DESeq2/edgeR results
Generate HTML or PDF reports for a set of genomic regions or DESeq2/edgeR results
Generating SAM file for PSMs in shotgun proteomics data
Generating Tree Hierarchy Visualizations from Gene Expression Data
Generating Tree Hierarchy Visualizations from Gene Expression Data
Gene Set Enrichment Analysis Extended to Contingency Cubes
Gene Set Enrichment Analysis (GSEA) of RNA-Seq Data: integrating differential expression and splicing
Gene Set Enrichment Analysis (GSEA) of RNA-Seq Data: integrating differential expression and splicing
Gene Set Enrichment For ChIP-seq Peak Data
Gene Set Enrichment / Projection Displays
Gene Set Enrichment / Projection Displays
Gene set over-representation, enrichment and network analyses for high-throughput screens
Gene-Specific Phenotype EstimatoR
GenoMetric Query Language for R/Bioconductor
GenoMetric Query Language for R/Bioconductor
Genomic trajectories with heterogeneous genetic and environmental backgrounds
Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation
Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation
Graphical User Interface for IsoCorrectoR
Graphical User Interface for IsoCorrectoR
GUIDE-seq analysis pipeline
Handling and analysis of high-throughput microbiome census data
Handling and analysis of high-throughput microbiome census data
HDF5 backend for DelayedArray objects
HDF5 backend for DelayedArray objects
Hierarchical Gating Pipeline for flow cytometry data
Hierarchical Gating Pipeline for flow cytometry data
Hits Selection for Synthetic Lethal RNAi Screen Data
HLA typing clustering and visualization based on specific similarity metrics
HLA typing clustering and visualization based on specific similarity metrics
iASeq: integrating multiple sequencing datasets for detecting allele-specific events
Identification of cancer cell lines based on their weighted mutational/ variational fingerprint
Identification of cancer cell lines based on their weighted mutational/ variational fingerprint
Identification of cancer cell lines based on their weighted mutational/ variational fingerprint
Identification of candidate causal perturbations from differential gene expression data
Identification of candidate causal perturbations from differential gene expression data
Identification of genetic Variants affecting Alternative Splicing
Identifies cell population in flow cytometry data.
Identify, Annotate and Visualize Alternative Splicing and Isoform Switches with Functional Consequences from both short- and long-read RNA-seq data.
Identify, Annotate and Visualize Alternative Splicing and Isoform Switches with Functional Consequences from both short- and long-read RNA-seq data.
Identify Contaminants in Marker-gene and Metagenomics Sequencing Data
Identify Differentially Expressed Genes from RNA-seq data
Identify likely duplicate samples from genomic or meta-data
Identify likely duplicate samples from genomic or meta-data
Identify likely duplicate samples from genomic or meta-data
immune Cell Analysis Tool
immunoClust - Automated Pipeline for Population Detection in Flow Cytometry
Implementation of the differential equation model described in "Dynamical modelling of phenotypes in a genome-wide RNAi live-cell imaging assay"
Import and summarize transcript-level estimates for transcript- and gene-level analysis
Import and summarize transcript-level estimates for transcript- and gene-level analysis
Import, process and analysis of Time-of-Flight Secondary Ion Mass Spectrometry (ToF-SIMS) imaging data
Improves Early Build Genome Assemblies using Strand-Seq Data
Improves Early Build Genome Assemblies using Strand-Seq Data
Imputation-guided re-construction of complete methylomes from WGBS data
Imputation-guided re-construction of complete methylomes from WGBS data
Imputation-guided re-construction of complete methylomes from WGBS data
Independent Hypothesis Weighting
Independent Hypothesis Weighting
Inference and visualisation of Single-Cell RNA-seq data as a hierarchical tree structure
Inference of differential exon usage in RNA-Seq
Inference of differential exon usage in RNA-Seq
Inferring metabolic networks from untargeted high-resolution mass spectrometry data
Inferring metabolic networks from untargeted high-resolution mass spectrometry data
Infers biological signatures from gene expression data
Infers clonal composition of a tumor
Infrastructure for representing and interacting with gated and ungated cytometry data sets.
Infrastructure for representing and interacting with gated and ungated cytometry data sets.
InPAS: a bioconductor package for the identification of novel alternative PolyAdenylation Sites (PAS) using RNA-seq data
InPAS: a bioconductor package for the identification of novel alternative PolyAdenylation Sites (PAS) using RNA-seq data
Integrated Copy Number Variation detection
Integrating Cap Enrichment with Transcript Expression Analysis
Integrating Cap Enrichment with Transcript Expression Analysis
Integrative analysis of Multi-omics data for Alternative Splicing
Integrative Statistics of alleLe Dependent Expression
Interactive Analysis of Single Cell RNA-Seq Data
Interactive Analysis of Single Cell RNA-Seq Data
Interactive Analysis of Single Cell RNA-Seq Data
Interactive Differential Expresion Analysis Browser
Interactive Differential Expresion Analysis Browser
Interactive Differential Expression AnaLysis
Interactive Differential Expression AnaLysis
Interactive Differential Expression AnaLysis
Interactive SummarizedExperiment Explorer
Interactive SummarizedExperiment Explorer
Interactive SummarizedExperiment Explorer
Interactive SummarizedExperiment Explorer
Interactive Visualization of Integrated Differential Expression and Differential Network Analysis for Biomarker Candidate Selection Package
Interactive Visualization of Integrated Differential Expression and Differential Network Analysis for Biomarker Candidate Selection Package
Interactive Visualization of RNA-seq Data Using a Principal Components Approach
Interactive Visualization of RNA-seq Data Using a Principal Components Approach
Interfaces the tandem protein identification algorithm in R
Interface to the RDP Classifier
Intron-Exon Retention Estimator
Intron-Exon Retention Estimator
Investigation of Fragmentation Conditions in Top-Down Proteomics
Investigation of Fragmentation Conditions in Top-Down Proteomics
iSEE Universe
iSEE Universe
iSEE Universe
Iteratively Adjusted Surrogate Variable Analysis
Iteratively Adjusted Surrogate Variable Analysis
Iteratively Adjusted Surrogate Variable Analysis
JunctionSeq: A Utility for Detection of Differential Exon and Splice-Junction Usage in RNA-Seq data
KnowSeq R/Bioc package: Beyond the traditional Transcriptomic pipeline
KnowSeq R/Bioc package: Beyond the traditional Transcriptomic pipeline
L1-regularization based methods for detection of differential splicing
L1-regularization based methods for detection of differential splicing
Label-free data analysis pipeline for optimal identification and quantitation
LC-MS and GC-MS Data Analysis
LC-MS and GC-MS Data Analysis
LC-MS and GC-MS Data Analysis
LC-MS/MS Differential Expression Tests
Linear model and normality based normalization and transformation method (Linnorm)
Linear Models for Microarray Data
Lipid and Oxylipin Biomarker Screening through Adduct Hierarchy Sequences
LoomExperiment container
LoomExperiment container
Machine Learning Interface for RNA-Seq Data
Machine Learning Interface for RNA-Seq Data
Make read coverage plots from BigWig files
Make read coverage plots from BigWig files
Manipulate Zarr archives as R objects
Manipulating and exploring protein and proteomics data
Manipulating and exploring protein and proteomics data
Mapping cell populations in flow cytometry data for cross-sample comparisons using the Friedman-Rafsky Test
Marker Gene Finder in RNA-seq data
Massive correlating biclusters for gene expression data and associated methods
Massive correlating biclusters for gene expression data and associated methods
Massive correlating biclusters for gene expression data and associated methods
Mass spectrum processing by wavelet-based algorithms
Matching and meta-clustering in flow cytometry
Maximum Likelihood Decay Modeling of RNA Degradation Data
Maximum Likelihood Decay Modeling of RNA Degradation Data
Meta-analysis for the metagenomic read counts data from different cohorts
Meta-analysis of RNA-Seq count data in multiple studies
Metab: An R Package for a High-Throughput Analysis of Metabolomics Data Generated by GC-MS.
MetaCyto: A package for meta-analysis of cytometry data
Methods for Single-Cell RNA-Seq Data Analysis
Methods for Single-Cell RNA-Seq Data Analysis
Methods to Find the Gene Expression Modules that Represent the Drivers of Kauffman's Attractor Landscape
Methylated CpGs Set Enrichment Analysis
Methylated CpGs Set Enrichment Analysis
Methylation-Based Inference of Regulatory Activity
Methylation-Based Inference of Regulatory Activity
Microbial Assemblage Normalized Transcript Analysis
Microbial Assemblage Normalized Transcript Analysis
MiRNA Ranking by Gene Expression
Mixture modeling of single-cell RNA-seq data to identify genes with differential distributions
Mixture modeling of single-cell RNA-seq data to identify genes with differential distributions
Mixture Models for Single-Cell Assays
Mixture Models for Single-Cell Assays
Model higher-order methylation profiles
Model higher-order methylation profiles
Monte Carlo Reference-based Consensus Clustering
Monte Carlo Reference-based Consensus Clustering
MS-based metabolomics annotation pipeline
MS-based metabolomics annotation pipeline
MS-based metabolomics annotation pipeline
msgbsR: methylation sensitive genotyping by sequencing (MS-GBS) R functions
Multi-Dataset Model-based Differential Expression Proteomics Analysis Platform
Multi-Dataset Model-based Differential Expression Proteomics Analysis Platform
Multilevel Model for Multivariate Responses with Missing Values
Multi-sample multi-group scRNA-seq data analysis tools
Multi-sample multi-group scRNA-seq data analysis tools
Multi-sample multi-group scRNA-seq data analysis tools
Navigating mass spectral similarity in high-resolution MS/MS metabolomics data
Navigating mass spectral similarity in high-resolution MS/MS metabolomics data
ncdfFlow: A package that provides HDF5 based storage for flow cytometry data.
ncdfFlow: A package that provides HDF5 based storage for flow cytometry data.
Negative Binomial Models to detect Differential Splicing
Negative Binomial Models to detect Differential Splicing
NGScopy: Detection of Copy Number Variations in Next Generation Sequencing sequencing
Non-parametric Flow Cytometry Data Gating
Normalization of single cell RNA-seq data
Normalization of single cell RNA-seq data
ODE add-on to CellNOptR
Omics Data Integration Project
Omics Data Integration Project
Omics Data Integration Project
One-Dimensional Soli-Expression by Nonlinear Stochastic Embedding (OneSENSE)
ontological exploration of scRNA-seq of 1.3 million mouse neurons from 10x genomics
Open Reading Frames in Genomics
Open Reading Frames in Genomics
Open Reading Frames in Genomics
Open-source toolkit to analyse data from xCELLigence System (RTCA)
Optimal p-value weighting with independent information
Oscope - A statistical pipeline for identifying oscillatory genes in unsynchronized single cell RNA-seq
OUTRIDER - OUTlier in RNA-Seq fInDER
OUTRIDER - OUTlier in RNA-Seq fInDER
PAIRADISE: Paired analysis of differential isoform expression
PAIRADISE: Paired analysis of differential isoform expression
Parameter Optimization for Flow Cytometry Data Transformation
parser for netCDF, mzXML, mzData and mzML and mzIdentML files (mass spectrometry data)
parser for netCDF, mzXML, mzData and mzML and mzIdentML files (mass spectrometry data)
Parsing pepXML files and filter based on peptide FDR.
PathoStat Statistical Microbiome Analysis Package
PathoStat Statistical Microbiome Analysis Package
PCA, PLS(-DA) and OPLS(-DA) for multivariate analysis and feature selection of omics data
Perform a maximum contrast projection of 3D images along the z-dimension into 2D
Permutation-Based Analysis associating Conserved Differentially Methylated Elements Across Multiple Generations to a Treatment Effect
Permutation-Based Analysis associating Conserved Differentially Methylated Elements Across Multiple Generations to a Treatment Effect
PGCA: An Algorithm to Link Protein Groups Created from MS/MS Data
PharmacOGenomics Ontology Support
Phenotyping Flow Cytometry Assays
Phylogenetic partitioning based ILR transform for metagenomics data
Phylogenetic partitioning based ILR transform for metagenomics data
pipeline for single cell RNA-seq data analysis
pipeline for single cell RNA-seq data analysis
Plotting functions for derfinder
Plotting functions for derfinder
Posterior association networks and functional modules inferred from rich phenotypes of gene perturbations
Power Estimation Tool for RNA-Seq and proteomics data
Prediction of gestational age with Illumina HumanMethylation450 data
Prediction of pri-miRNA Transcription Start Site
Prediction of pri-miRNA Transcription Start Site
Predict metabolic pathway activity based on metabolomics data
Prize: an R package for prioritization estimation based on analytic hierarchy process
Probe region expression estimation for RNA-seq data for improved microarray comparability
Projection-based Gating Strategy Optimization for Flow and Mass Cytometry
PROspective Power Evaluation for RNAseq
Protein Significance Analysis in DDA, SRM and DIA for Label-free or Label-based Proteomics Experiments
Protein Significance Analysis in DDA, SRM and DIA for Label-free or Label-based Proteomics Experiments
Protein Significance Analysis in DDA, SRM and DIA for Label-free or Label-based Proteomics Experiments
Protein Significance Analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling
Protein Significance Analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling
Provides a GUI for DAPAR
Provides a GUI for DAPAR
Provides a GUI for rTANDEM
Publication-ready volcano plots with enhanced colouring and labeling
Publication-ready volcano plots with enhanced colouring and labeling
Quality Control for Single-Cell RNA-seq Data
Quality Control of Gated Flow Cytometry Experiments
Quantification and Visulization of Variations of Splicing in Population
Quantification and Visulization of Variations of Splicing in Population
Quantification and Visulization of Variations of Splicing in Population
Quantification and Visulization of Variations of Splicing in Population
Quantify and Annotate Short Reads in R
Quantify and Annotate Short Reads in R
Quantify and interpret divers of variation in multilevel gene expression experiments
Quantify and interpret divers of variation in multilevel gene expression experiments
qusage: Quantitative Set Analysis for Gene Expression
Read density map construction and accession. Visualization of ChIPSeq and RNASeq data sets
Reconstruction, visualization and analysis of branching trajectories
Reconstruction, visualization and analysis of branching trajectories
Reconstruction, visualization and analysis of branching trajectories
Remove Unwanted Variation from RNA-Seq Data
Report of DEG analysis
Report of DEG analysis
Representation and manipulation of short genomic alignments
Representation and manipulation of short genomic alignments
Reproducibility-Optimized Test Statistic
Reproducible GSEA Benchmarking
Reproducible GSEA Benchmarking
R Interface to the metaviz web app for interactive metagenomics data analysis and visualization
R Interface to the metaviz web app for interactive metagenomics data analysis and visualization
R Interface to the ProteomeXchange Repository
R Interface to the ProteomeXchange Repository
RNA-seq data analysis using the Poisson-Tweedie family of distributions
RNAseq data simulation, differential expression analysis and performance comparison of differential expression methods
RNAseq data simulation, differential expression analysis and performance comparison of differential expression methods
RNASeqR: an R package for automated two-group RNA-Seq analysis workflow
RNASeqR: an R package for automated two-group RNA-Seq analysis workflow
RNASeqR: an R package for automated two-group RNA-Seq analysis workflow
RnaSeqSampleSize
rnaSeq secondary analyses
RnBeads
Robust prediction of clinical outcomes using cytometry data without cell gating
R package for the statistical assessment of cell state hierarchies from single-cell RNA-seq data
S4 Classes for Single Cell Data
S4 Classes for Single Cell Data
S4 Classes for Single Cell Data
samExploreR package: high-performance read summarisation to count vectors with avaliability of sequencing depth reduction simulation
Sample Classifier
Sample size for RNAseq studies
scDataviz: single cell dataviz and downstream analyses
scDataviz: single cell dataviz and downstream analyses
Seamless navigation through combined results of set-based and network-based enrichment analysis
Seamless navigation through combined results of set-based and network-based enrichment analysis
Search for correlation between epigenetic signals and gene expression in TADs
Search for correlation between epigenetic signals and gene expression in TADs
Semantic labelling of flow cytometric cell populations
Semantic labelling of flow cytometric cell populations
Sensitive and highly resolved identification of RNA-protein interaction sites in PAR-CLIP data
Shiny app GUI wrapper for ggplot with built-in statistical analysis
Shrinkage estimation of dispersion in Negative Binomial models for RNA-seq experiments with small sample size
SigFuge
SigFuge
Significance-based Modules Integrating the Transcriptome and Epigenome
Significance-based Modules Integrating the Transcriptome and Epigenome
Similarity measures for chemical compounds
Simple Simulation of Single-cell RNA Sequencing Data
Simple Simulation of Single-cell RNA Sequencing Data
Simple Simulation of Single-cell RNA Sequencing Data
Simple Simulation of Single-cell RNA Sequencing Data
Simulating Whole-Genome Inherited Bisulphite Sequencing Data
Simulating Whole-Genome Inherited Bisulphite Sequencing Data
Simulating Whole-Genome Inherited Bisulphite Sequencing Data
Single-Cell Analysis Toolkit for Gene Expression Data in R
Single-Cell Analysis Toolkit for Gene Expression Data in R
Single-Cell Consensus Clustering
Single-Cell Consensus Clustering
Single Cell Differential Expression
Single-cell Interpretation via Multi-kernel LeaRning (SIMLR)
Single Cell Overview of Normalized Expression data
Single Cell Overview of Normalized Expression data
Single cell replicability analysis
Single cell replicability analysis
Single-cell RNA sequencing data normalization
Single-cell RNA sequencing data normalization
Single Cell RNA-Seq UMI Filtering Facilitator (scruff)
Single Cell RNA-Seq UMI Filtering Facilitator (scruff)
Single Cell RNA-Seq UMI Filtering Facilitator (scruff)
Single Cell RNA-Seq UMI Filtering Facilitator (scruff)
Single Cell RNA-Seq UMI Filtering Facilitator (scruff)
Single Cell RNA-Seq UMI Filtering Facilitator (scruff)
Single Cell Shiny Application for Analysing Single Cell Transcriptomics Data
Single-channel array normalization (SCAN) and Universal exPression Codes (UPC)
Sparse Data Observations for Simulating Synthetic Abundance
Splice event prediction and quantification from RNA-seq data
Splice event prediction and quantification from RNA-seq data
Splice Interpreter of Transcripts
Splice Interpreter of Transcripts
Stability Ranking
Statistical analysis for sparse high-throughput sequencing
Statistical analysis for sparse high-throughput sequencing
Statistical analysis for the Colony Formation Assay
Statistical analysis for the Colony Formation Assay
Statistical Analysis of High-Throughput Genetic Perturbation Screens
Statistical Analysis of High-Throughput Genetic Perturbation Screens
Statistical Analysis of High-Throughput Genetic Perturbation Screens
Statistical Analysis of High-Throughput Genetic Perturbation Screens
Statistical Analysis of High-Throughput Genetic Perturbation Screens
Statistical analysis of high-throughput RNAi screens
Statistical Analysis of Metabolomic Data
Statistical Analysis of Molecular Profiles
Statistical Analysis of Molecular Profiles
Statistical Analysis of MPRA data
Statistical analysis of sequins
Statistical Inference of Associations between Microbial Communities And host phenoTypes
Statistical Inference of Associations between Microbial Communities And host phenoTypes
Statistical Inferences with MeDIP-seq Data (SIMD) to infer the methylation level for each CpG site
Statistical Inferences with MeDIP-seq Data (SIMD) to infer the methylation level for each CpG site
Statistical methods for the analysis of flow cytometry data
Statistical methods for the analysis of flow cytometry data
Statistical tools and data structures for plate-based flow cytometry
Statistics and dIagnostic Graphs for HTS
Subclonal copy number and LOH prediction from whole genome sequencing of tumours
Subclonal copy number and LOH prediction from whole genome sequencing of tumours
Subread Sequence Alignment and Counting for R
Subsampling of high-throughput sequencing count data
Suite of Functions for Pooled Crispr Screen QC and Analysis
Suite of Functions for Pooled Crispr Screen QC and Analysis
Suite of Functions for Pooled Crispr Screen QC and Analysis
Surrogate Variable Analysis
Surrogate Variable Analysis
SVAPLSseq-An R package to estimate the hidden factors of unwanted variability and adjust for them to enable a more powerful and accurate differential expression analysis based on RNAseq data
Switch-like differential expression across single-cell trajectories
systemPipeRdata: NGS workflow templates and sample data
systemPipeR: NGS workflow and report generation environment
systemPipeR: NGS workflow and report generation environment
Targeted Learning with Moderated Statistics for Biomarker Discovery
Targeted Learning with Moderated Statistics for Biomarker Discovery
TCC: Differential expression analysis for tag count data with robust normalization strategies
TCC: Differential expression analysis for tag count data with robust normalization strategies
Test for differential expression for RNA-seq data
The Cancer Genome Atlas Data Integration
The Discordant Method: A Novel Approach for Differential Correlation
The Genomic STate ANnotation Package
Time-Course Multi-Omics data integration
Time-Course Multi-Omics data integration
Time-Course Multi-Omics data integration
Tools for counting and visualising mutations in a target location
Tools for curating, analyzing, and manipulating biological sequences
Tools for high-throughput metabolomics
Tools for high-throughput metabolomics
Tools for making reports in various formats
Tools for making reports in various formats
Tools for processing of high-dimensional cytometry data
Tools for processing of high-dimensional cytometry data
Tools for qPLEX-RIME data analysis
Tools for qPLEX-RIME data analysis
Tools for spliced gene structure manipulation and analysis
Topology-based pathway analysis of RNA-seq data
Training of boolean logic models of signalling networks using prior knowledge networks and perturbation data
Training of boolean logic models of signalling networks using prior knowledge networks and perturbation data
Transcript expression inference and differential expression analysis for RNA-seq data
Transcriptional analysis based on transcriptograms
Transcriptional analysis based on transcriptograms
Transcript Quantification Import with Automatic Metadata
Transcript Quantification Import with Automatic Metadata
Transform and Filter SWATH Data for Statistical Packages
Transform and Filter SWATH Data for Statistical Packages
TRONCO, an R package for TRanslational ONCOlogy
TRONCO, an R package for TRanslational ONCOlogy
uORF prediction in R
Using Gaussian graphical structue learning estimation in generalized least squared regression for multivariate normal regression
Using Mass Cytometry for Differential Abundance Analyses
Using Mass Cytometry for Differential Abundance Analyses
uSORT: A self-refining ordering pipeline for gene selection
Utilities for Exploration and Assessment of Confidence of LC-MSn Proteomics Identifications
Utilities for Exploration and Assessment of Confidence of LC-MSn Proteomics Identifications
Utilities for flow cytometry
Utilities for flow cytometry
Utilities for Handling Single-Cell Droplet Data
Utilities for Handling Single-Cell Droplet Data
Variance stabilization in flow cytometry (and microarrays)
Visual and interactive gene expression analysis
Visual and interactive gene expression analysis
Visual and interactive gene expression analysis
Visual Exploration of Omic Datasets Using a Shiny App
Visual Exploration of Omic Datasets Using a Shiny App
Visual Exploration of Omic Datasets Using a Shiny App
Visualise microarray and RNAseq data using gene ontology annotations
Visualise microarray and RNAseq data using gene ontology annotations
Visualization for flow cytometry
Visualization of highly multiplexed imaging cytometry data in R
Visualization of highly multiplexed imaging cytometry data in R
Visualization of highly multiplexed imaging cytometry data in R
Visualization of multi-dimentional cancer genomics data
Visualize Cytometry data with ggplot
Visualize Cytometry data with ggplot
Workflow to process tandem MS files and build MassBank records
Wrap Command Tools and Pipelines Using CWL
Wrap Command Tools and Pipelines Using CWL
Zero-Inflated Negative Binomial Model for RNA-Seq Data
Zero-Inflated Negative Binomial Model for RNA-Seq Data