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

Software for analysis plots and data class for gated flow cytometry data.

Proper citation: flowPlots (RRID:SCR_002177) Copy   

•   Source: SciCrunch Registry

http://cran.r-project.org/web/packages/metaRNASeq/

Software package for meta-analysis of RNA-seq data. This package implements two p-value combination techniques (inverse normal and Fisher methods). It also provides a vignette explaining how to combine data from multiple RNA-seq experiments.

Proper citation: metaRNASeq (RRID:SCR_002174) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/src/contrib/Archive/demi/

R package for estimating differential expression from multiple indicators that capitalizes on the high number of concurrent measurements. It extends to various experimental designs and target categories (transcripts, genes, genomic regions) as well as small sample sizes.

Proper citation: DEMI (RRID:SCR_002291) Copy   

•   Source: SciCrunch Registry

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

A Bioconductor software package for high throughput flow cytometry that provides S4 data structures and basic functions.

Proper citation: flowCore (RRID:SCR_002205) Copy   

•   Source: SciCrunch Registry

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

Software package for the analysis of flow cytometry bead data. It extends flowCore to provide functionality specific to bead data. One of the goals of this package is to automate analysis of bead data for the purpose of normalization.

Proper citation: flowBeads (RRID:SCR_002440) Copy   

•   Source: SciCrunch Registry

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

A software package to analyze flow cytometric data using gate information to follow population / community dynamics.

Proper citation: flowCyBar (RRID:SCR_002319) Copy   

•   Source: SciCrunch Registry

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

Software package containing functions for allele-specific gene expression (ASE) analysis using meta-analysis based allele-specific expression detection.

Proper citation: MBASED (RRID:SCR_002584) Copy   

•   Source: SciCrunch Registry

http://jchempaint.github.io/

Chemical 2D structure editor and viewer application/applet based on the Chemistry Development Kit (CDK).

Proper citation: JChemPaint (RRID:SCR_000095) Copy   

•   Source: SciCrunch Registry

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

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software for semantic labelling of flow cytometric cell populations.

Proper citation: flowCL (RRID:SCR_000046) Copy   

•   Source: SciCrunch Registry

https://code.google.com/p/cbrowse/

Software providing an AJAX-based web browser for visualizing and analyzing transcriptome assemblies and contigs.

Proper citation: Cbrowse (RRID:SCR_000044) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/data/annotation/html/RmiR.Hs.miRNA.html

Software package for various databases of microRNA Targets.

Proper citation: RmiR.Hs.miRNA (RRID:SCR_000101) Copy   

•   Source: SciCrunch Registry

https://github.com/SciLifeLab/facs

Software for classification of Sequences using Bloom filters that can accurately and rapidly align sequences to a reference sequence.

Proper citation: FACS (RRID:SCR_000055) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/ngopt/

Software that produces high quality microbial genome assemblies on a laptop computer without any parameter tuning. A5-miseq does this by automating the process of adapter trimming, quality filtering, error correction, contig and scaffold generation, and detection of misassemblies. Unlike the original A5 pipeline, A5-miseq can use long reads from the Illumina MiSeq, use read pairing information during contig generation, and includes several improvements to read trimming.

Proper citation: A5-miseq (RRID:SCR_012148) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/plek/

An alignment-free software tool which uses a computational pipeline based on an improved k-mer scheme and a support vector machine (SVM) algorithm to distinguish lncRNAs from messenger RNAs (mRNAs), in the absence of genomic sequences or annotations. It is especially suitable for PacBio or 454 sequencing data and large-scale transcriptome data.

Proper citation: PLEK (RRID:SCR_012132) Copy   

•   Source: SciCrunch Registry

http://www.lifetechnologies.com/fr/fr/home/technical-resources/software-downloads/lifescope-genomic-analysis-software.html

Genomic Analysis Software designed to match the accuracy of the next generation 5500 Genetic Analyzers with Exact Call Chemistry (ECC).

Proper citation: LifeScope (RRID:SCR_013234) Copy   

•   Source: SciCrunch Registry

http://cran.r-project.org/web/packages/metaMA/

Software R package for meta-analysis for microarrays. It combines either p-values or modified effect sizes from different studies to find differentially expressed genes.

Proper citation: metaMA (RRID:SCR_000408) Copy   

•   Source: SciCrunch Registry

http://cran.r-project.org/web/packages/VennDiagram/

Software providing a set of functions to generate high-resolution Venn and Euler plots. Includes handling for several special cases, including two-case scaling, and extensive customization of plot shape and structure.

Proper citation: VennDiagram (RRID:SCR_002414) Copy   

•   Source: SciCrunch Registry

http://cran.r-project.org/web/packages/muma/

Software that provides guidelines for the whole process of metabolomic data interpretation, from data pre-processing, to dataset exploration and visualization, to identification of potentially interesting metabolites. Guidelines outline the following processes: preprocessing of high-throughput data (normalization and scalings); principal component analysis with help tool for choosing best-separating principal components and automatic testing for outliers; automatic univariate analysis for parametric and non-parametric data, with generation of specific reports (volcano and box plots); partial least square discriminant analysis (PLS-DA); orthogonal partial least square discriminant analysis (OPLS-DA); Statistical Total Correlation Spectroscopy (STOCSY); and Ratio Analysis Nuclear Magnetic Resonance (NMR) Spectroscopy (RANSY).

Proper citation: MUMA (RRID:SCR_002412) Copy   

•   Source: SciCrunch Registry

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

Software R package to model and impute non-detects in results of qPCR experiments.Used to directly model non-detects as missing data.

Proper citation: nondetects (RRID:SCR_001702) Copy   

•   Source: SciCrunch Registry

http://cran.r-project.org/web/packages/enviPick/

Software for sequential partitioning, clustering and peak detection of centroided LC-MS mass spectrometry data (.mzXML). Interactive result and raw data plot.

Proper citation: enviPick (RRID:SCR_003059) Copy   

•   Source: SciCrunch Registry