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

Software that identifies cell populations in Flow Cytometry data using non-parametric clustering and segmented-regression-based change point detection.

Proper citation: flowMeans (RRID:SCR_002275) Copy   

•   Source: SciCrunch Registry
  

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

Software for merging of mixture components for model-based automated gating of flow cytometry data using the flowClust framework.

Proper citation: flowMerge (RRID:SCR_002224) Copy   

•   Source: SciCrunch Registry
  

https://bioconductor.org/packages/2.11/bioc/html/flowPhyto.html

An R package that performs aggregate statistics on virtually unlimited collections of raw flow cytometry files and provides a memory efficient, parallelized solution for analyzing high-throughput flow cytometric data.

Proper citation: flowPhyto (RRID:SCR_002183) Copy   

•   Source: SciCrunch Registry
  

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

Software that implements all bioinformatics steps required for the quantitative, high-resolution analysis of DNA methylation patterns from bisulfite sequencing data.

Proper citation: BEAT (RRID:SCR_002387) Copy   

•   Source: SciCrunch Registry
  

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

A Bioconductor package integrating algorithms to extract compound spectra, annotate isotope and adduct peaks, and propose the accurate compound mass even in highly complex data.

Proper citation: CAMERA - Collection of annotation related methods for mass spectrometry data (RRID:SCR_002466) 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
  

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://github.com/powellgenomicslab/ascend

Software R package for analysis of single cell RNA-seq expression, normalization and differential expression data. Provides framework to perform cell and gene filtering, quality control, normalization, dimension reduction, clustering, differential expression, and visualization functions.

Proper citation: ascend (RRID:SCR_017257) Copy   

•   Source: SciCrunch Registry
  

https://scfind.sanger.ac.uk/

Software R package as search tool for single cell RNA-seq data by gene lists. Builds index from scRNA-seq datasets which organizes information in suitable and compact manner so that datasets can be very efficiently searched for either cells or cell types in which given list of genes is expressed.

Proper citation: Scfind (RRID:SCR_017339) 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://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://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/2.11/bioc/html/easyRNASeq.html

Software that calculates the coverage of high-throughput short-reads against a genome of reference and summarizes it per feature of interest (e.g. exon, gene, transcript). The data can be normalized as ''RPKM'' or by the ''DESeq'' or ''edgeR'' package.

Proper citation: easyRNASeq (RRID:SCR_012020) Copy   

•   Source: SciCrunch Registry
  

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

Genotype Calling and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.

Proper citation: CRLMM (RRID:SCR_012580) Copy   

•   Source: SciCrunch Registry
  

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

Software for normalization of Agilent miRNA arrays.

Proper citation: LVSmiRNA (RRID:SCR_012752) Copy   

•   Source: SciCrunch Registry
  

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

Software package that detects statistically significant difference between read enrichment profiles in different ChIP-Seq samples.

Proper citation: MMDiff (RRID:SCR_012692) Copy   

•   Source: SciCrunch Registry