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

An MCMC-based algorithm that uses next-generation sequencing data to estimate tumor purity and clonality for paired tumor-normal data.

Proper citation: PurBayes (RRID:SCR_002068) Copy   

•   Source: SciCrunch Registry

http://figshare.com/articles/Tool_for_rapid_annotation_of_microbial_SNPs_TRAMS_a_simple_program_for_rapid_annotation_of_genomic_variation_in_prokaryotes_/782261

A software program for functional annotation of genomic single nucleotide polymorphisms (SNPs) which is available to download as a single file executable for WINDOWS users with limited computational experience and as a Python script for Mac OS and Linux users. It needs only a tab delimited text file containing SNP locations, reference nucleotide and SNPs in different strains along with a reference genome sequence in standard GenBank or EMBL format. It annotates SNPs as synonymous, non-synonymous or nonsense. Non-synonymous SNPs in start and stop codons are separated as non-start and non-stop SNPs, respectively. SNPs in overlapping features are annotated separately for each feature and multiple nucleotide polymorphisms (MNPs) within a codon are combined prior to annotation. A workflow has also been developed for use in Galaxy to map short reads to a reference genome and extract and annotate the SNPs.

Proper citation: TRAMS (RRID:SCR_002003) Copy   

•   Source: SciCrunch Registry

http://drpowell.github.io/vennt/

A web-tool to generate dynamic Venn diagrams for differential gene expression.

Proper citation: Vennt (RRID:SCR_002083) Copy   

•   Source: SciCrunch Registry

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

An R/Bioconductor package for quality assessment of target enrichment experiments. This package provides functionalities for assessing and visualizing the quality of the target enrichment process, like specificity and sensitivity of the capture, per-target read coverage and so on.

Proper citation: TEQC (RRID:SCR_001943) Copy   

•   Source: SciCrunch Registry

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

Software that provides visualization tools for flow cytometry data.

Proper citation: flowViz (RRID:SCR_002075) Copy   

•   Source: SciCrunch Registry

https://www.bioconductor.org/packages//2.11/bioc/html/flowQB.html

A fully automated R Bioconductor package to calculate automatically the detector efficiency (Q), optical background (B) and intrinsic CV of the beads.

Proper citation: flowQB (RRID:SCR_002144) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/voxbo

Software package for brain image manipulation and analysis, focusing on fMRI and lesion analysis. VoxBo can be used independently or in conjunction with other packages. It provides GLM-based statistical tools, an architecture for interoperability with other tools (they encourage users to incorporate SPM and FSL into their processing pipelines), an automation system, a system for parallel distributed computing, numerous stand-alone tools, decent wiki-based documentation, and lots more.

Proper citation: VoxBo (RRID:SCR_002166) Copy   

•   Source: SciCrunch Registry

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

A Bioconductor package designed to perform quantitative analysis of cell proliferation in tracking dye-based experiments. The package uses an R implementation of the Levenberg-Marquardt algorithm (minpack.lm) to fit a set of peaks (corresponding to different generations of cells) over the proliferation-tracking dye distribution in a FACS experiment.

Proper citation: flowFit (RRID:SCR_002286) Copy   

•   Source: SciCrunch Registry

http://fiji.sc

Software package as distribution of ImageJ and ImageJ2 together with Java, Java3D and plugins organized into coherent menu structure. Used to assist research in life sciences.

Proper citation: Fiji (RRID:SCR_002285) Copy   

•   Source: SciCrunch Registry

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

An easy-to-use R package for classification of alternative splicing and prediction of coding potential from RNA-seq data.

Proper citation: spliceR (RRID:SCR_002280) Copy   

•   Source: SciCrunch Registry

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.nitrc.org/projects/nptk/

Non-rigid registration / distortion correction tools for enhanced functional localization through the registration of EPI fMRI to high-resolution anatomical MRI.

Proper citation: NPTK (RRID:SCR_002496) Copy   

•   Source: SciCrunch Registry

http://www.ncdc.noaa.gov/paleo/softlib/paleovu.html

A complete browse and visualization tool for all types of paleoclimate and paleoecological data (Version 1.0 for Windows 3.1 and the Macintosh). Point and click to create queries, list site information, display or plot variables and data, or export the data for further processing and analysis. Note: PaleoVu is no longer maintained or supported. Data content is not being updated, and compatibility problems may exist with newer operating systems. PaleoVu is still suitable as a teaching tool, but our internet-based browsing tools are the most up to date source for paleoclimatic data.

Proper citation: PaleoVu (RRID:SCR_002411) 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.med.unc.edu/bric/ideagroup/free-softwares/hammer

Software for both groupwise registration and longitudinal registration, which are the necessary steps for many brain-related applications. Specifically, groupwise registration is important for unbiased analysis of a large set of MR brain images. Therefore, in this software package, they have included two of their recently-developed groupwise registration algorithms: 1) Improved unbiased groupwise registration guided with the sharp group-mean image, and 2) Hierarchical feature-based groupwise registration with implicit template (Groupwise-HAMMER for short). On the other hand, they also included their recently-developed groupwise longitudinal registration algorithm that aligns not only the longitudinal image sequence for each subject, but also align all longitudinal image sequences of all subjects to the common space simultaneously.

Proper citation: GLIRT (RRID:SCR_002390) Copy   

•   Source: SciCrunch Registry

https://github.com/BRAINSia/BRAINSTools/tree/master/BRAINSFit

A program for registering images with with mutual information based metric. Several registration options are given for 3,6, 9,12,16 parameter (i.e. translate, rigid, scale, scale/skew, full affine) based constraints for the registration. The program uses the Slicer3 execution model framework to define the command line arguments and can be fully integrated with Slicer3 using the module discovery capabilities of Slicer3

Proper citation: BRAINSFit (RRID:SCR_002340) Copy   

•   Source: SciCrunch Registry