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

Software package that is an implementation of the BayesPeak algorithm for peak-calling in ChIP-seq data.

Proper citation: BayesPeak (RRID:SCR_013011) Copy   

•   Source: SciCrunch Registry

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

Software that identifies protein binding sites from ChIP-seq and nucleosome positioning experiments.

Proper citation: ChIPseqR (RRID:SCR_013016) Copy   

•   Source: SciCrunch Registry

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

Software functions for reading aCGH data from image analysis output files and clone information files, creation of aCGH S3 objects for storing these data. Basic methods for accessing/replacing, subsetting, printing and plotting aCGH objects.

Proper citation: aCGH (RRID:SCR_013232) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/2.1/bioc/html/arrayMagic.html

Software providing a collection of utilities for quality control and processing of two-colour cDNA microarray data

Proper citation: arrayMagic (RRID:SCR_010933) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/2.6/bioc/html/DEGseq.html

R package to identify differentially expressed genes from RNA-Seq data.

Proper citation: DEGseq (RRID:SCR_008480) Copy   

•   Source: SciCrunch Registry

https://www.bioconductor.org/packages/release/bioc/html/GSVA.html

Open source software R package for assaying variation of gene set enrichment over sample population.Used for microarray and RNA-seq data analysis. Gene set enrichment method that estimates variation of pathway activity over sample population in unsupervised manner.

Proper citation: GSVA (RRID:SCR_021058) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/SimFFPE/

Software R package to simulate artifact chimeric reads specifically generated in next generation sequencing process of formalin fixed paraffin embedded tissue. Simulates normal reads as well as artifact chimeric reads that are enriched in FFPE samples. These artifact chimeric reads can lead to large amounts of false positive structural variant calls.

Proper citation: SimFFPE (RRID:SCR_021085) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/release/bioc/html/PhenStat.html

Software R package for statistical analysis of phenotypic data.Tool kit for standardized analysis of high throughput phenotypic data.

Proper citation: PhenStat (RRID:SCR_021317) Copy   

•   Source: SciCrunch Registry

https://github.com/PapenfussLab/svaNUMT

Software R package for Nuclear Mitochondrial integration events NUMT detection using structural variant calls.

Proper citation: svaNUMT (RRID:SCR_021381) Copy   

•   Source: SciCrunch Registry

http://master.bioconductor.org/packages/2.13/bioc/html/BHC.html

Software package that performs bottom-up hierarchical clustering, using a Dirichlet Process (infinite mixture) to model uncertainty in the data and Bayesian model selection to decide at each step which clusters to merge. This avoids several limitations of traditional methods, for example how many clusters there should be and how to choose a principled distance metric. This implementation accepts multinomial (i.e. discrete, with 2+ categories) or time-series data and also includes a randomised algorithm which is more efficient for larger data sets.

Proper citation: BHC (RRID:SCR_006399) Copy   

•   Source: SciCrunch Registry

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

A software package that provides functions to read raw RT-qPCR data of different platforms.

Proper citation: ReadqPCR (RRID:SCR_000030) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/epialleleR/

Software R package for calling hypermethylated variant epiallele frequencies at level of genomic regions or individual cytosines in next-generation sequencing data using binary alignment map files as input. Used for sensitive allele specific methylation analysis in next generation sequencing data. Used for sensitive detection, quantification and visualisation of mosaic epimutations in methylation sequencing data.

Proper citation: epialleleR (RRID:SCR_023913) Copy   

•   Source: SciCrunch Registry

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

Software application for discovering direct or indirect targets of transcription factors (TFs) using ChIP-chip or ChIP-seq, and microarray or RNA-seq gene expression data. Inputting a list of genes of potential targets of one TF from ChIP-chip or ChIP-seq, and the gene expression results, it generates a regulatory network of the TF.

Proper citation: GeneNetworkBuilder (RRID:SCR_006455) Copy   

•   Source: SciCrunch Registry

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

R package with tools that use probabilistic inference of ChIP-Seq. It follows an empirical Bayes mixture model approach.

Proper citation: PICS (RRID:SCR_001093) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/release/bioc/html/DESeq2.html

Software package for differential gene expression analysis based on the negative binomial distribution. Used for analyzing RNA-seq data for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates.

Proper citation: DESeq2 (RRID:SCR_015687) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/EGAD/

Software package implements series of highly efficient tools to calculate functional properties of networks based on guilt by association methods. Ultra fast functional analysis of gene networks.

Proper citation: Extending Guilt by Association by Degree (RRID:SCR_018427) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/AUCell/

Software R package to identify cells with active gene sets in single cell RNA-seq data. Used for analysis of gene set activity in single cell RNA-seq data.Used to calculate whether critical subset of input gene set is enriched within expressed genes for each cell.

Proper citation: AUCell (RRID:SCR_021327) Copy   

•   Source: SciCrunch Registry

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

Software package that provides utility functions to manage and analyse MS2/MS3 fragmentation data from ion trap mass spectrometry. It was designed for high throughput metabolomics data with many biological samples and a large numer of ion trees collected. Tests have been done with data from low-resolution mass spectrometry but could be readily extended to precursor ion based fragmentation data from high resoultion mass spectrometry.

Proper citation: iontree (RRID:SCR_002813) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/StructuralVariantAnnotation/

Software R package for structural variant analysis. Contains helper functions for dealing with structural variants in VCF format. Contains functions for parsing VCFs from number of popular callers as well as functions for dealing with breakpoints involving two separate genomic loci encoded as GRanges objects.

Proper citation: StructuralVariantAnnotation (RRID:SCR_018683) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/EnhancedVolcano/

Software R package to produce publication ready volcano plots with enhanced colouring and labeling. Used to visualise results of differential expression analyses.

Proper citation: EnhancedVolcano (RRID:SCR_018931) Copy   

•   Source: SciCrunch Registry