Biocview "ImmunoOncology"

A GAM based framework for analysis of ChIP-Seq data
A GAM based framework for analysis of ChIP-Seq data
Analysis for short time-series data
Analysis for short time-series data
Analysis for short time-series data
Analysis Of Differential Abundance Taking Sample Variation Into Account
Analyze isomiRs and miRNAs from small RNA-seq
Analyze Transcription Factor Enrichment
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
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
An package for identification of novel peptides by customized database derived from RNA-Seq
A package for the analysis of GC-MS metabolite profiling data
A package for the analysis of GC-MS metabolite profiling data
Assessment of duplication rates in RNA-Seq datasets
Assessment of duplication rates in RNA-Seq datasets
A suite of functions to facilitate zFPKM transformations
ATAC-seq Quality Control
ATAC-seq Quality Control
A tool to use GO Subtrees to Tag and Annotate Genes within a set
Automatic and interactive quality control for flow cytometry data
Batch Effects Quality Control Software
Bayesian Analysis of Single-Cell Sequencing data
Better prediction by use of co-data: Adaptive group-regularized ridge regression
Breakpoint analysis of time-course expression data
Breakpoint analysis of time-course expression data
Bump Hunter
Bump Hunter
Bump Hunter
Calculate strandness information of a bam file
Calculate strandness information of a bam file
Cancer Clone Finder
chroGPS2: Generation, visualization and differential analysis of epigenome maps
Chromatin Variation Across Regions
Codon Usage Analysis and Prediction of Gene Expressivity
Codon Usage Analysis and Prediction of Gene Expressivity
Co-Expression Analysis of Sequencing Data
Co-expression Modules identification Tool
Co-expression Modules identification Tool
Compare Characteristic Features of Count Data Sets
Coordinate Covariation Analysis
Coordinate Covariation Analysis
Coordinate Covariation Analysis
Coordinated Gene Activity in Pattern Sets
Copy number calling and SNV classification using targeted short read sequencing
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
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
Cross omic genetic fingerprinting
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
DeepBlueR
DeepBlueR
derfinder helper package
derfinder helper package
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
Differential Co-expression Analysis
Differential expression analysis and model fitting for single-cell RNA-seq data
Differential expression analysis of longitudinal count data sets
Differential gene expression analysis based on the negative binomial distribution
Empirical Analysis of Digital Gene Expression Data in R
Engineering Evaluation by Gene Categorization (eegc)
Epigenetic Dissection of Intra-Sample-Heterogeneity
Epigenetic Dissection of Intra-Sample-Heterogeneity
Explore and download data from the recount project
Explore and download data from the recount project
Fast Correlation Based Filter for Feature Selection
Filter replicated high-throughput transcriptome sequencing data
flowClean
Functions to conduct quality control analysis in methylation data
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
Gene Set Enrichment Analysis (GSEA) of RNA-Seq Data: integrating differential expression and splicing
GenoMetric Query Language for R/Bioconductor
Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation
Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation
Graphical User Interface for IsoCorrectoR
HDF5 backend for DelayedArray objects
HDF5 backend for DelayedArray objects
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 Novel alternative PolyAdenylation Sites (PAS)
Identification of Novel alternative PolyAdenylation Sites (PAS)
Identify Differentially Expressed Genes from RNA-seq data
immunoClust - Automated Pipeline for Population Detection in Flow Cytometry
Import and summarize transcript-level estimates for transcript- and gene-level analysis
Integrative analysis pipeline for pooled CRISPR functional genetic screens
Integrative analysis pipeline for pooled CRISPR functional genetic screens
Interactive Analysis of Single Cell RNA-Seq Data
Interactive Differential Expresion Analysis Browser
Intron-Exon Retention Estimator
Intron-Exon Retention Estimator
Iteratively Adjusted Surrogate Variable Analysis
Iteratively Adjusted Surrogate Variable Analysis
Linear Models for Microarray Data
Meta-analysis of RNA-Seq count data in multiple studies
Microbiome Analytics
Microbiome Analytics
Monte Carlo Reference-based Consensus Clustering
Multi-Dataset Model-based Differential Expression Proteomics Analysis Platform
Negative Binomial Models to detect Differential Splicing
Negative Binomial Models to detect Differential Splicing
Normalization of single cell RNA-seq data
Normalization of single cell RNA-seq data
Omics Data Integration Project
PathoStat Statistical Microbiome Analysis Package
PathoStat Statistical Microbiome Analysis Package
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
Plotting functions for derfinder
Plotting functions for derfinder
Publication-ready volcano plots with enhanced colouring and labeling
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
Report of DEG analysis
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
RNASeqR: RNA-Seq workflow for case-control study
RNASeqR: RNA-Seq workflow for case-control study
RNASeqR: RNA-Seq workflow for case-control study
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
SigFuge
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 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)
Splice event prediction and quantification from RNA-seq data
Splice event prediction and quantification from RNA-seq data
Statistical analysis for the Colony Formation Assay
Statistical Inferences with MeDIP-seq Data (SIMD) to infer the methylation level for each CpG site
Subclonal copy number and LOH prediction from whole genome sequencing of tumours
Subread sequence alignment and counting for R
Targeted Learning with Moderated Statistics for Biomarker Discovery
Tools for high-throughput metabolomics
Tools for high-throughput metabolomics
Training of boolean logic models of signalling networks using prior knowledge networks and perturbation data
Transcriptional analysis based on transcriptograms
Transcriptional analysis based on transcriptograms
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
Utilities for Exploration and Assessment of Confidence of LC-MSn Proteomics Identifications
Utilities for Exploration and Assessment of Confidence of LC-MSn Proteomics Identifications
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
Visualise microarray and RNAseq data using gene ontology annotations