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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
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
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
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
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
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
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
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
https://bioconductor.org/packages/KEGGgraph/
Software R package interface between KEGG pathway and graph object as well as collection of tools to analyze, dissect and visualize these graphs.
Proper citation: KEGGgraph (RRID:SCR_023788) Copy
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
http://bioconductor.org/packages/release/bioc/html/topGO.html
Software package which provides tools for testing GO terms while accounting for the topology of the GO graph. Different test statistics and different methods for eliminating local similarities and dependencies between GO terms can be implemented and applied.
Proper citation: topGO (RRID:SCR_014798) Copy
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
https://bioconductor.org/packages/Orthology.eg.db/
Software R package to provide orthology mappings between species, based on NCBI Gene IDs and NCBI orthology mappings.
Proper citation: Orthology.eg.db (RRID:SCR_024740) Copy
https://www.bioconductor.org/packages/release/bioc/html/ExperimentHub.html
Software R package provides central location where curated data from experiments, publications or training courses can be accessed.
Proper citation: ExperimentHub (RRID:SCR_024820) Copy
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