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

Software package for efficient manipulation of biological strings. Memory efficient string containers, string matching algorithms, and other utilities, for fast manipulation of large biological sequences or sets of sequences.

Proper citation: Biostrings (RRID:SCR_016949) Copy   

•   Source: SciCrunch Registry
  

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

Software written in R for determining cluster count and membership by stability evidence in unsupervised analysis. Provides quantitative and visual stability evidence for estimating the number of unsupervised classes in a dataset with item tracking, item consensus and cluster consensus plots.

Proper citation: ConsensusClusterPlus (RRID:SCR_016954) Copy   

•   Source: SciCrunch Registry
  

http://bioconductor.org/packages/GenomicFeatures/

Software R package for making and manipulating transcript centric annotations. Used to download the genomic locations of the transcripts, exons and cds of a given organism, from either the UCSC Genome Browser or a BioMart database.

Proper citation: GenomicFeatures (RRID:SCR_016960) Copy   

•   Source: SciCrunch Registry
  

https://github.com/SofieVG/FlowSOM

Software tool to analyze Flow or mass cytometry data using a Self-Organizing Map. Used to obtain an overview of how all markers are behaving on all cells, and to detect subsets that might be missed otherwise.

Proper citation: FlowSOM (RRID:SCR_016899) Copy   

•   Source: SciCrunch Registry
  

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

Software R package for multivariate analysis and feature selection of omics data. Used for visualization, regression, classification, and feature selection of omics data where the number of variables exceeds the number of samples and with multicollinearity among variables.

Proper citation: ropls (RRID:SCR_016888) Copy   

•   Source: SciCrunch Registry
  

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

Software application for performing Gene Ontology analysis on RNAseq data and other length biased data. Used to reduce complexity and highlight biological processes in genome wide expression studies.

Proper citation: Goseq (RRID:SCR_017052) Copy   

•   Source: SciCrunch Registry
  

http://bioconductor.org/packages/GenomicRanges/

Software R package for computing and annotating genomic ranges. Used for storing and manipulating genomic intervals and variables defined along genome.

Proper citation: Genomic Ranges (RRID:SCR_017051) 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
  

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
  

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

Software package that identifies differential expression in high-throughput ''count'' data, such as that derived from next-generation sequencing machines.

Proper citation: baySeq (RRID:SCR_012795) Copy   

•   Source: SciCrunch Registry
  

http://bioconductor.org/packages/devel/bioc/html/RPA.html

A fully scalable online pre-processing algorithm for short oligonucleotide microarray atlases.

Proper citation: RPA (RRID:SCR_012768) Copy   

•   Source: SciCrunch Registry
  

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

Software that provides an integrated solution for the Illumina microarray data analysis.

Proper citation: lumi (RRID:SCR_012781) Copy   

•   Source: SciCrunch Registry
  

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

This software package implements the QUBIC algorithm for the qualitative biclustering with gene expression data.

Proper citation: rqubic (RRID:SCR_012869) Copy   

•   Source: SciCrunch Registry
  

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

Compute differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data. Also enables occupancy (overlap) analysis and plotting functions.

Proper citation: DiffBind (RRID:SCR_012918) Copy   

•   Source: SciCrunch Registry
  

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

A bi-clustering algorithm which is optimizes for binary data analysis.

Proper citation: iBBiG (RRID:SCR_012882) Copy   

•   Source: SciCrunch Registry
  

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

A biclustering method; it finds correlated blocks (transcription modules) in gene expression (or other tabular) data.

Proper citation: eisa (RRID:SCR_012883) Copy   

•   Source: SciCrunch Registry
  

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

Software providing a fast scatterplot smoother suitable for microarray normalization based on B-splines with second-order difference penalty. Functions for microarray normalization of single-colour data i.e. Affymetrix/Illumina and two-colour data supplied as marray MarrayRaw-objects or limma RGList-objects are available.

Proper citation: TurboNorm (RRID:SCR_012963) Copy   

•   Source: SciCrunch Registry