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http://sourceforge.net/projects/genseng/

Software for detecting copy number variations from next generation sequencing data. Used to identify regions of discrete copy number changes while simultaneously accounting for effects of multiple confounders.

Proper citation: GENSENG (RRID:SCR_000378) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/limsforproteomi/

Laboratory information management system for proteomics. The software works with 2DPAGE-based proteomics workflow.

Proper citation: LIPAGE (RRID:SCR_000290) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/virema/

Software Python package for detection, alignment and reporting of recombination events in Next-Generation Sequencing data. Detects and reports recombination or fusion events in virus genomes using deep sequencing datasets.

Proper citation: ViReMa (RRID:SCR_000566) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/sparseassembler/

Software for memory-efficient genome assembly. It utilizes sparse k-mer.

Proper citation: SparseAssembler (RRID:SCR_001100) Copy   

•   Source: SciCrunch Registry

https://gitlab.sib.swiss/EPD/chipseq

Set of software modules for performing common ChIP-seq data analysis tasks across the whole genome, including positional correlation analysis, peak detection, and genome partitioning into signal-rich and signal-poor regions. The tools are designed to be simple, fast and highly modular. Each program carries out a well-defined data processing procedure that can potentially fit into a pipeline framework. ChIP-Seq is also freely available on a Web interface.

Proper citation: ChIP-seq (RRID:SCR_001237) Copy   

•   Source: SciCrunch Registry

http://dti-tk.sourceforge.net/pmwiki/pmwiki.php

A spatial normalization and atlas construction toolkit optimized for examining white matter morphometry using DTI data with special care taken to respect the tensorial nature of the data. It implements a state-of-the-art registration algorithm that drives the alignment of white matter (WM) tracts by matching the orientation of the underlying fiber bundle at each voxel. The algorithm has been shown to both improve WM tract alignment and to enhance the power of statistical inference in clinical settings. A 2011 study published in NeuroImage ranks DTI-TK the top-performing tool in its class. Key features include: * open standard-based file IO support: NIfTI format for scalar, vector and tensor image volumes * tool chains for manipulating tensor image volumes: resampling, smoothing, warping, registration & visualization * pipelines for WM morphometry: spatial normalization & atlas construction for population-based studies * built-in cluster-computing support: support for open source Sun Grid Engine (SGE) * Interoperability with other popular DTI tools: AFNI, Camino, FSL & DTIStudio * Interoperability with ITK-SNAP: support multi-modal visualization and segmentation

Proper citation: Diffusion Tensor Imaging ToolKit (RRID:SCR_001642) Copy   

•   Source: SciCrunch Registry

http://mged.sourceforge.net/ontologies/MGEDontology.php

An ontology including concepts, definitions, terms, and resources for a standardized description of a microarray experiment in support of MAGE v.1. The MGED ontology is divided into the MGED Core ontology which is intended to be stable and in synch with MAGE v.1; and the MGED Extended ontology which adds further associations and classes not found in MAGE v.1. These terms will enable structure queries of elements of the experiments. Furthermore, the terms will also enable unambiguous descriptions of how the experiment was performed.

Proper citation: MGED Ontology (RRID:SCR_004484) Copy   

•   Source: SciCrunch Registry

http://solexaqa.sourceforge.net/

Software package to calculate sequence quality statistics and create visual representations of data quality for Illumina's second-generation sequencing technology.

Proper citation: SolexaQA (RRID:SCR_005421) Copy   

•   Source: SciCrunch Registry

http://sybil.sourceforge.net/

A web-based software package for comparative genomics.

Proper citation: Sybil (RRID:SCR_005593) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/openadam/

A web-based database management system for the large amount of genotype data generated from the Affymetrix GeneChip Mapping Array and Genome-Wide Human SNP Array platforms.

Proper citation: openADAM (RRID:SCR_002018) Copy   

•   Source: SciCrunch Registry

http://snver.sourceforge.net/

Statistical software tool for calling common and rare variants in analysis of pool or individual next-generation sequencing data. This software is optimized for analysis of whole-exome sequencing data and whole-genome sequencing data.

Proper citation: SNVer (RRID:SCR_002061) Copy   

•   Source: SciCrunch Registry

http://rubioseq.sourceforge.net/

Stand-alone and multiplatform application for the integrated analysis of NGS data. It implements pipelines for the analysis of single nucleotide and copy-number variation and bisulfite-seq and ChIP-seq experiments.

Proper citation: RUbioSeq (RRID:SCR_002508) Copy   

•   Source: SciCrunch Registry

http://migen.sourceforge.net/

Standard specification for the information required to report a genotyping experiment, covering: study and experiment design, subject information, genotyping procedure, and data analysis methods. The goal is to set a reporting standard for adoption by the research community to facilitate consistent data interpretation and independent validation/reproduction, and to serve as guidance for database design for storing genotyping experiment data. MIGen is being developed as a collaborative project involving international domain experts and is a registered project under MIBBI: Minimum Information for Biological and Biomedical Investigations.

Proper citation: MIGen (RRID:SCR_006959) Copy   

•   Source: SciCrunch Registry

http://samtools.sourceforge.net/

A generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms.

Proper citation: SAM format (RRID:SCR_012093) Copy   

•   Source: SciCrunch Registry

http://hollow.sourceforge.net/

HOLLOW facilitates the production of surface images of proteins. HOLLOW is a portable command-line utility written in Python 2.4-2.7; it does not have any other dependencies (although running under the PyPy JIT interpreter, it runs much faster). The input is a PDB file. The output is a PDB file of dummy water atoms that forms a cast of the voids and channels of a protein. HOLLOW generates a surface from a cast of the protein surface. HOLLOW fills the interior spaces of a protein structure with dummy atoms defined on an overlapping grid. The surface generated by these dummy atoms can be shown to reproduce the surface of the protein at the ideal limit. The use of the surface of the dummy atoms allows us to focus on a specific piece of the interior surface. Simply by deleting dummy atoms, the interior surface can be trimmed to produce a custom portion of the interior space. For advanced coloring of the surface, the B-factor of the dummy atoms can be calculated as the average of the B-factor of the protein atoms surrounding the dummy atoms. This allows various colorings of the surface to be conveyed through the B-factor field of the PDB files. The volume filling representation facilitated by HOLLOW is meant to complement other programs that identify voids, pockets and channels, such as SPHGEN and CASTp, which identify binding sites but cannot produce output that can be rendered in standard molecular graphics software. HOLLOW can be used to help render these binding pockets.

Proper citation: HOLLOW (RRID:SCR_005729) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/tracker/?group_id=76834&atid=835555

Open Biomedical Ontologies Tracker that allows users to browse the Plant Ontology (PO) term requests and view their status. Details include a summary, ID, status, Date opened, assignee, submitter, resolution and assigned priority. New requests are accepted from logged in users.

Proper citation: OBO Tracker: Plant Ontology (PO) TERM requests (RRID:SCR_006497) Copy   

•   Source: SciCrunch Registry

http://hanalyzer.sourceforge.net/

An open-source data integration system designed to assist biologists in explaining the results observed in genome-scale experiments as well as generating new hypotheses. It combines information extraction techniques, semantic data integration, and reasoning and facilitates network visualization. The Hanalyzer source code and binaries are available for download.

Proper citation: Hanalyzer (RRID:SCR_000923) Copy   

•   Source: SciCrunch Registry

https://www.ebi.ac.uk/chebi/beta/

Collection of chemical compounds and other small molecular entities that incorporates an ontological classification of chemical compounds of biological relevance, whereby the relationships between molecular entities or classes of entities and their parents and/or children are specified. The molecular entities in question are either products of nature or synthetic products used to intervene in the processes of living organisms.

Proper citation: CHEBI (RRID:SCR_002088) Copy   

•   Source: SciCrunch Registry

http://genevenn.sourceforge.net/

A web application creating Venn diagrams from two or three gene lists.

Proper citation: GeneVenn (RRID:SCR_012117) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/magnolya/

A software which enables copy number variation (CNV) detections without using a reference genome. Magnolya directly compares the two next-generation sequences datasets.

Proper citation: Magnolya (RRID:SCR_000164) Copy   

•   Source: SciCrunch Registry