Tools   Select Another Resource Report Type

http://bamview.sourceforge.net/

A free interactive display of read alignments in BAM data files that can be launched with Java Web Start or downloaded. This interactive Java application for visualizing the large amounts of data stored for sequence reads which are aligned against a reference genome sequence can be used in a number of contexts including SNP calling and structural annotation. It has been integrated into Artemis so that the reads can be viewed in the context of the nucleotide sequence and genomic features. The source code is available as part of the Artemis code which can be downloaded from GitHub.

Proper citation: BamView (RRID:SCR_004207) Copy   

•   Source: SciCrunch Registry
  

http://noble.gs.washington.edu/proj/genomedata/

A format for efficient storage of multiple tracks of numeric data anchored to a genome. The format allows fast random access to hundreds of gigabytes of data, while retaining a small disk space footprint. They have also developed utilities to load data into this format. Retrieving data from this format is more than 2900 times faster than a naive approach using wiggle files. A reference implementation in Python and C components is available here under the GNU General Public License. The software has only been tested on Linux and Mac systems.

Proper citation: Genomedata (RRID:SCR_004544) Copy   

•   Source: SciCrunch Registry
  

http://omicsoft.com/osa/

A fast and accurate alignment tool for RNA-Seq data.

Proper citation: Omicsoft Sequence Aligner (RRID:SCR_005270) Copy   

•   Source: SciCrunch Registry
  

http://www.timelogic.com/catalog/799/velocimapper

Accelerated alignment tool for mapping data from next-generation DNA sequencing systems. It runs on TimeLogic''s newest FPGA-based DeCypher J-Series Similarity Search Engine Accelerator to provide fast and reliable results that significantly outperform software-only or GPU-accelerated alternatives.

Proper citation: VelociMapper (RRID:SCR_005262) Copy   

•   Source: SciCrunch Registry
  

http://linux1.softberry.com/spldb/SpliceDB.html

Database of canonical and non-canonical mammalian splice sites. The information about verified splice site sequences for canonical and non-canonical sites is presented with the supporting evidence. Weight matrices were built for the major splice groups, which can be incorporated into gene prediction programs.

Proper citation: SpliceDB (RRID:SCR_006262) Copy   

•   Source: SciCrunch Registry
  

http://www.pathxl.com/pathxl-research/pathxl-tma

Tissue microarray (TMA) Software used for Biomarker Discovery that allows TMA experiments to be performed anytime, anywhere, reducing administrative costs and time. It is designed to support TMA scoring workflow and allows configuration of experiments in minutes. Access and view clinical metadata, the TMA core, scoring criteria and the TMA map all on a single interface.

Proper citation: PathXL TMA (RRID:SCR_005596) Copy   

•   Source: SciCrunch Registry
  

http://www.dnabaser.com/download/chromatogram-explorer/

A Windows Explorer clone dedicated to DNA sequence analysis and manipulation. View, edit, and convert chromatograms. Trim low quality ends automatically. The Lite version of Chromatogram Explorer is freeware.

Proper citation: DNA Chromatogram Explorer (RRID:SCR_005585) Copy   

•   Source: SciCrunch Registry
  

http://www.clcbio.com/products/clc-main-workbench/

A suite of software for DNA, RNA and protein sequence data analysis. The software allows for the analysis and visualization of Sanger sequencing data as well as gene expression analysis, molecular cloning, primer design, phylogenetic analyses, and sequence data management.

Proper citation: CLC Main Workbench (RRID:SCR_000354) Copy   

•   Source: SciCrunch Registry
  

http://nucleobytes.com/index.php/4peaks

Software application for viewing and editing sequence trace files.

Proper citation: 4Peaks (RRID:SCR_000015) Copy   

•   Source: SciCrunch Registry
  

https://mzmatch.sourceforge.net/MetAssign.php

Software that combines information from the mass-to-charge ratio, retention time and intensity of each peak, together with a model of the inter-peak dependency structure, to increase the accuracy of peak annotation. The software has been implemented as part of the mzMatch metabolomics analysis pipeline, which is available for download.

Proper citation: MetAssign (RRID:SCR_000092) 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://code.google.com/p/annotare/

A software tool for annotating biomedical investigations and the resulting data, then producing a MAGE-TAB file. This software is a standalone desktop which features: an editor function, an annotation modifier, incorporation of terms from biomedical ontologies, standard templates for common experiment types, a design aid to help create a new document, and a validator that checks for syntactic and semantic violations.

Proper citation: Annotare (RRID:SCR_000319) Copy   

•   Source: SciCrunch Registry
  

http://apps.cytoscape.org/apps/pepper

A Cytoscape app designed to identify protein pathways / complexes as densely connected subnetworks from seed lists of proteins derived from pull-down assays (i.e AP-MS...).

Proper citation: PEPPER (RRID:SCR_000431) Copy   

•   Source: SciCrunch Registry
  

Issue

https://cran.r-project.org/web/packages/adegenet/index.html

Software package dedicated to the handling of molecular marker data for multivariate analysis. This package is related to ADE4, a R package for multivariate analysis, graphics, phylogeny and spatial analysis. (entry from Genetic Analysis Software)

Proper citation: ADEGENET (RRID:SCR_000825) Copy   

•   Source: SciCrunch Registry
  

https://pypi.python.org/pypi/illuminate/

Python module and utilities to parse the metrics binaries output by Illumina sequencers, and provides usable data in the form of python dictionaries and dataframes. Intended to emulate the output of Illumina SAV, it allows you to print sequencing run metrics to the command line as well as work with the data programmatically.

Proper citation: Illuminate (RRID:SCR_000178) Copy   

•   Source: SciCrunch Registry
  

http://sourceforge.net/projects/ngs-cleaner/

Software application that provides cleaning of FASTQ/A formatted large DNA sequence files containing multiple short-reads sequences provided by Next Generation Sequencing platforms.

Proper citation: NGS-Cleaner (RRID:SCR_000574) Copy   

•   Source: SciCrunch Registry
  

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

Software package that implements and enhances circular visualization in R. Due to natural born feature of R to draw statistical graphics, this package can provide more general and flexible way to visualize huge information in circular style.

Proper citation: circlize (RRID:SCR_002141) Copy   

•   Source: SciCrunch Registry
  

http://gusevlab.org/projects/germline/

Software application for discovering long shared segments of Identity by Descent (IBD) between pairs of individuals in a large population. It takes as input genotype or haplotype marker data for individuals (as well as an optional known pedigree) and generates a list of all pairwise segmental sharing., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: GERMLINE (RRID:SCR_001720) 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