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http://www.bioconductor.org/packages/release/bioc/html/affy.html

Software R package of functions and classes for the analysis of oligonucleotide arrays manufactured by Affymetrix. Used to process probe level data and for exploratory oligonucleotide array analysis.

Proper citation: affy (RRID:SCR_012835) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/sva.html

Contains functions for removing batch effects and other unwanted variation in high-throughput experiment.

Proper citation: sva package (RRID:SCR_012836) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/devel/bioc/html/TargetScore.html

Software to infer the posterior distributions of microRNA targets by probabilistically modelling the likelihood microRNA-overexpression fold-changes and sequence-based scores.

Proper citation: TargetScore (RRID:SCR_012933) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/2.12/bioc/html/RLMM.html

A Genotype Calling Algorithm for Affymetrix SNP Arrays.

Proper citation: RLMM (RRID:SCR_012984) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/2.12/bioc/html/charm.html

Software package that implements analysis tools for DNA methylation data generated using Nimblegen microarrays and the McrBC protocol.

Proper citation: charm (RRID:SCR_012992) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/2.12/bioc/html/BiSeq.html

Software package that provides useful classes and functions to handle and analyze targeted bisulfite sequencing (BS) data such as reduced-representation bisulfite sequencing (RRBS) data.

Proper citation: BiSeq (RRID:SCR_012993) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/2.12/bioc/html/MEDME.html

Software that allows the prediction of absolute and relative methylation levels based on measures obtained by MeDIP-microarray experiments.

Proper citation: MEDME (RRID:SCR_012995) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/2.12/bioc/html/Rolexa.html

Software that provides probabilistic base calling, quality checks and diagnostic plots for Solexa sequencing data.

Proper citation: Rolexa (RRID:SCR_013017) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/2.12/bioc/html/cn.mops.html

A data processing pipeline for copy number variations and aberrations (CNVs and CNAs) from next generation sequencing (NGS) data.

Proper citation: cn.mops (RRID:SCR_013036) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages//2.10/bioc/html/HiTC.html

Software package to explore high-throughput ''C'' data such as 5C or Hi-C.

Proper citation: HiTC (RRID:SCR_013175) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/2.9/bioc/html/Repitools.html

Software tools for the analysis of enrichment-based epigenomic data.

Proper citation: Repitools (RRID:SCR_013242) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages//2.10/bioc/html/CancerMutationAnalysis.html

Software package that implements gene and gene-set level analysis methods for somatic mutation studies of cancer.

Proper citation: CancerMutationAnalysis (RRID:SCR_013181) Copy   

•   Source: SciCrunch Registry

http://msstats.org/

A package for statistical relative quantification of proteins and peptides in global, targeted, and data-independent proteomics. It handles shotgun, label-free, and label-based Selected Reaction Monitoring, as well as SWATH/DIA (Data Independent Acquisition) experiments. MSStats provide functionality for data processing and visualization, model-based statistical analysis, and model-based sample size calculations.

Proper citation: MSstats (RRID:SCR_014353) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/scTHI/

Software R package to identify active pairs of ligand receptors from single cells in order to study,among others, tumor host interactions. Contains set of signatures to classify cells from tumor microenvironment.

Proper citation: scTHI (RRID:SCR_018918) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/variancePartition/

Software R package to quantify and interpret divers of variation in multilevel gene expression experiments.Provides statistical and visualization framework for studying drivers of variation in RNA-seq datasets in many types of high throughput genomic assays including RNA-seq gene-, exon- and isoform-level quantification, splicing efficiency, protein quantification, metabolite quantification, metagenomic assays, methylation arrays and epigenomic sequencing assays.

Proper citation: variancePartition (RRID:SCR_019204) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/synergyfinder/

Software R package as efficient implementations for all popular synergy scoring models for drug combinations, including HSA, Loewe, Bliss and ZIP and visualization of synergy scores as either two dimensional or three dimensional interaction surface over dose matrix. Used to calculate and visualize synergy scores for drug combinations.

Proper citation: SynergyFinder (RRID:SCR_019318) Copy   

•   Source: SciCrunch Registry

https://sydneybiox.github.io/CiteFuse/

Software R package consisting of suite of tools for doublet detection, modality integration, clustering, differential RNA and protein expression analysis, antibody-derived tag evaluation, ligand-receptor interaction analysis and interactive web-based visualization of CITE-seq data.

Proper citation: CiteFuse (RRID:SCR_019321) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/2.12/bioc/html/DNAcopy.html

Software that segments DNA copy number data using circular binary segmentation to detect regions with abnormal copy number.

Proper citation: DNAcopy (RRID:SCR_012560) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/release/bioc/html/MetaCyto.html

Software tool for automated meta-analysis of mass and flow cytometry data. Provides functions for preprocessing, automated gating and meta-analysis of cytometry data and collection of cytometry data from the ImmPort database.

Proper citation: MetaCyto (RRID:SCR_016415) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/ggtree/

Software R package for visualization and annotation of phylogenetic trees with their covariates and other tree like structures with their annotation data. Can import evolutionary data from different tree file formats and analysis programs as well as other associated data from experiments so that various sources and types of data can be displayed on tree for comparison and further analyses.

Proper citation: ggtree (RRID:SCR_018560) Copy   

•   Source: SciCrunch Registry