Tools   Select Another Resource Report Type

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

Software providing methods for segmenting, normalising and processing aCGH data; including plotting functions for visualising raw and segmented data for individual and multiple arrays.

Proper citation: snapCGH (RRID:SCR_012947) Copy   

•   Source: SciCrunch Registry

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

Software package that provides pathway enrichment techniques for miRNA expression data.

Proper citation: miRNApath (RRID:SCR_012833) Copy   

•   Source: SciCrunch Registry

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

Contains functions for removing batch effects and other unwanted variation in high-throughput experiment.

Proper citation: sva package (RRID:SCR_012836) Copy   

•   Source: SciCrunch Registry

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

A R package that enables the identification of protein binding footprints in DNase I hypersensitive sites sequencing (DNase-seq) data.

Proper citation: DNaseR (RRID:SCR_012819) Copy   

•   Source: SciCrunch Registry

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

Software to infer the posterior distributions of microRNA targets by probabilistically modelling the likelihood microRNA-overexpression fold-changes and sequence-based scores.

Proper citation: TargetScore (RRID:SCR_012933) Copy   

•   Source: SciCrunch Registry

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

A Genotype Calling Algorithm for Affymetrix SNP Arrays.

Proper citation: RLMM (RRID:SCR_012984) Copy   

•   Source: SciCrunch Registry

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

Software package that implements analysis tools for DNA methylation data generated using Nimblegen microarrays and the McrBC protocol.

Proper citation: charm (RRID:SCR_012992) Copy   

•   Source: SciCrunch Registry

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

Software package that provides useful classes and functions to handle and analyze targeted bisulfite sequencing (BS) data such as reduced-representation bisulfite sequencing (RRBS) data.

Proper citation: BiSeq (RRID:SCR_012993) Copy   

•   Source: SciCrunch Registry

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

Software that allows the prediction of absolute and relative methylation levels based on measures obtained by MeDIP-microarray experiments.

Proper citation: MEDME (RRID:SCR_012995) Copy   

•   Source: SciCrunch Registry

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

Software that provides probabilistic base calling, quality checks and diagnostic plots for Solexa sequencing data.

Proper citation: Rolexa (RRID:SCR_013017) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/2.12/bioc/html/cn.mops.html

A data processing pipeline for copy number variations and aberrations (CNVs and CNAs) from next generation sequencing (NGS) data.

Proper citation: cn.mops (RRID:SCR_013036) Copy   

•   Source: SciCrunch Registry

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

Software package to make access to the compilation of metadata from NCBI SRA and tools associated with submission, study, sample, experiment and run much more feasible. This is accomplished by parsing all the NCBI SRA metadata into a SQLite database that can be stored and queried locally. Fulltext search in the package make querying metadata very flexible and powerful. fastq and sra files can be downloaded for doing alignment locally. Beside ftp protocol, the SRAdb has funcitons supporting fastp protocol (ascp from Aspera Connect) for faster downloading large data files over long distance. The SQLite database is updated regularly as new data is added to SRA and can be downloaded at will for the most up-to-date metadata.

Proper citation: SRAdb (RRID:SCR_006524) Copy   

•   Source: SciCrunch Registry

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

A software package for the discovery of regulatory regions from Bis-seq data.

Proper citation: MethylSeekR (RRID:SCR_006513) Copy   

•   Source: SciCrunch Registry

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

Software to infer alternative splicing from paired-end RNA-seq data. The model is based on counting paths across exons, rather than pairwise exon connections, and estimates the fragment size and start distributions non-parametrically, which improves estimation precision.

Proper citation: casper (RRID:SCR_006613) Copy   

•   Source: SciCrunch Registry

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

A R package designed to improve ChIP-seq and ChIP-chip target gene ranking using publicly available gene expression data. It takes as input predicted transcription factor (TF) bound genes from ChIPx data and uses a corresponding database of gene expression profiles downloaded from NCBI GEO to rank the TF bound targets in order of which gene is most likely to be functional TF target.

Proper citation: ChIPXpress (RRID:SCR_006653) Copy   

•   Source: SciCrunch Registry

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

Software package that provides quantitative variant callers for detecting subclonal mutations in ultra-deep (>=100x coverage) sequencing experiments. The algorithm is used for a comparative setup with a control experiment of the same loci and uses a beta-binomial model and a likelihood ratio test to discriminate sequencing errors and subclonal SNVs (single nucleotide variants).

Proper citation: deepSNV (RRID:SCR_006214) Copy   

•   Source: SciCrunch Registry

http://watson.nci.nih.gov/bioc_mirror/packages/2.11/bioc/html/EDASeq.html

Software for numerical and graphical summaries of RNA-Seq read data. Within-lane normalization procedures to adjust for GC-content effect (or other gene-level effects) on read counts: loess robust local regression, global-scaling, and full-quantile normalization (Risso et al., 2011). Between-lane normalization procedures to adjust for distributional differences between lanes (e.g., sequencing depth): global-scaling and full-quantile normalization (Bullard et al., 2010)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: EDASeq (RRID:SCR_006751) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/2.11/bioc/html/ShortRead.html

Software package for input, quality assessment and exploration of high-throughput sequence data. Used for input, quality assurance, and basic manipulation of `short read'' DNA sequences such as those produced by Solexa, 454, and related technologies, including exible import of common short read data formats.

Proper citation: ShortRead (RRID:SCR_006813) Copy   

•   Source: SciCrunch Registry

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

A statistical software package for identifying protein-associated transcripts from RIP-seq experiments. Infer and discriminate RIP peaks from RIP-seq alignments using two-state HMM with negative binomial emission probability. While RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides a suite of bioinformatics tools integrated within this self-contained software package comprehensively addressing issues ranging from post-alignments processing to visualization and annotation.

Proper citation: RIPSeeker (RRID:SCR_006810) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/2.9/bioc/html/RamiGO.html

Software package with an R interface sending requests to AmiGO visualize, retrieving DAG GO trees, parsing GraphViz DOT format files and exporting GML files for Cytoscape. Also uses RCytoscape to interactively display AmiGO trees in Cytoscape.

Proper citation: RamiGO (RRID:SCR_006922) Copy   

•   Source: SciCrunch Registry