Tools   Select Another Resource Report Type

http://www.bioconductor.org/packages/2.13/bioc/html/ChAMP.html

Software package that includes quality control metrics, a selection of normalization methods and novel methods to identify differentially methylated regions and to highlight copy number aberrations.

Proper citation: ChAMP (RRID:SCR_012891) Copy   

•   Source: SciCrunch Registry

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

Statistical tools for the analysis of ChIP-seq data.

Proper citation: CSAR (RRID:SCR_012930) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/2.13/bioc/html/CSSP.html

Software for power computation for ChIP-Seq data based on Bayesian estimation for local poisson counting process.

Proper citation: CSSP (RRID:SCR_012932) Copy   

•   Source: SciCrunch Registry

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

Software package that provides functions to identify genomic regions of interest based on segmented copy number data from multiple samples.

Proper citation: cghMCR (RRID:SCR_012898) Copy   

•   Source: SciCrunch Registry

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

Software using a non-parametric method for identifying differentially expressed (up- or down- regulated) genes based on the estimated percentage of false predictions (pfp).

Proper citation: RankProd (RRID:SCR_013046) Copy   

•   Source: SciCrunch Registry

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

Software developed for analyzing data derived from methylated DNA immunoprecipitation (MeDIP) experiments followed by sequencing (MeDIP-seq).

Proper citation: MEDIPS (RRID:SCR_012996) 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

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

Software package that facilitates the primary analysis of ChIP-chip data.

Proper citation: Ringo (RRID:SCR_012973) Copy   

•   Source: SciCrunch Registry

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

Software for handling and analysis of high-throughput microbiome census data.

Proper citation: phyloseq (RRID:SCR_013080) Copy   

•   Source: SciCrunch Registry

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://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

http://www.fhcrc.org/

Fred Hutchinson Cancer Research Center and Seattle Cancer Care Alliance (SCCA) have merged to form Fred Hutchinson Cancer Center, unified adult cancer research and care center. Independent, nonprofit organization is clinically integrated part of UW Medicine and is UW Medicine’s cancer program.

Proper citation: Fred Hutchinson Cancer Center (RRID:SCR_004984) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://r3cseq.genereg.net/Site/index.html

An R/Bioconductor package to identify chromosomal interaction regions generated by chromosome conformation capture (3C) coupled to next-generation sequencing (NGS), a technique termed 3C-seq. It performs data analysis for a number of different experimental designs, as it can analyze 3C-seq data with or without a control experiment and it can be used to facilitate data analysis for experiments with multiple replicates. The r3Cseq package provides functions to perform data normalization, statistical analysis for cis/trans interactions and visualization in order to help scientists identify genomic regions that physically interact with the given viewpoints of interest. This tool greatly facilitates hypothesis generation and the interpretation of experimental results.

Proper citation: r3Cseq (RRID:SCR_003198) Copy   

•   Source: SciCrunch Registry

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

Software package for low-throughput real-time quantitative PCR data analysis. The package allows you to import easily qPCR data files. Thereafter, you can calculate amplification efficiencies, relative quantities and their standard errors, normalization factors based on the best reference genes choosen (using the SLqPCR package), and then the normalized relative quantities, the NRQs scaled to your control and their standard errors.

Proper citation: EasyqpcR (RRID:SCR_003406) Copy   

•   Source: SciCrunch Registry

https://scicrunch.org/resolver/SCR_002250

THIS RESOURCE IS NO LONGER IN SERVICE. Documented Jul 19, 2024. Metadatabase manually curated that provides web accessible tools related to genomics, transcriptomics, proteomics and metabolomics. Used as informative directory for multi-omic data analysis.

Proper citation: OMICtools (RRID:SCR_002250) Copy   

•   Source: SciCrunch Registry

http://bioinfo.cipf.es/noiseq/doku.php?id=start

Software used for the identification of differentially expressed genes from count data or previously normalized count data. It empirically models the noise distribution of count changes by contrasting fold-change differences (M) and absolute expression differences (D) for all the features in samples within the same condition. This reference distribution is then used to assess whether the M-D values computed between two conditions for a given gene is likely to be part of the noise or represent a true differential expression.

Proper citation: NOISeq (RRID:SCR_003002) Copy   

•   Source: SciCrunch Registry