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http://sourceforge.net/projects/sparseassembler/
Software for memory-efficient genome assembly. It utilizes sparse k-mer.
Proper citation: SparseAssembler (RRID:SCR_001100) Copy
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
http://sourceforge.net/projects/blox/
A quantitative medical imaging and visualization program for use on brain MR, DTI, and MRS data. Programming Language: Java, JavaScript, Scheme
Proper citation: Blox (RRID:SCR_006667) Copy
http://bionerds.sourceforge.net/
A named entity recognizer for the recovery of bioinformatics databases and software from primary literature. The entity recognizer achieved an F-measure of between 63% and 91% on different datasets (63%78% at the document level). Results from full-text literature analysis for both Genome Biology and BMC Bioinformatics journals are available as well as a full list of references and links for the various major resources mentioned. Data generated data can be used for exploration of bioinformatics database and software usage. This tool makes heavy use of GATE (version 6.1). It can be run in sandbox mode, which means a installation of GATE is not a prerequisite, but you will instead need to point the config to a unzipped gate_plugins directory instead (located in the bin/BMC_Files directory).
Proper citation: bioNerDS (RRID:SCR_006784) Copy
http://deconseq.sourceforge.net/
Software tool to automatically detect and efficiently remove sequence contaminations from genomic and metagenomic datasets. It is easily configurable and provides a user-friendly interface. The user can upload FASTA or FASTQ files and select the databases used for contamination screening, including seven human genomes, bacterial genomes, and viral genomes. The user can set the thresholds interactivly and see the results directly using the functionality of the graphical interface. The results can be downloaded in joined or separated files in different formats. The coverage-identity plots provide additional information that can guide the selections of the thresholds using color coded points and connecting lines.
Proper citation: DeconSeq (RRID:SCR_007006) Copy
http://fmatoolbox.sourceforge.net
Matlab toolbox used to help analyze electrophysiological and behavioral data recorded from freely moving animals.
Proper citation: FMAToolbox (RRID:SCR_015533) Copy
http://sourceforge.net/projects/metavar/
Software package that enables detection of sequence variation between metagenomic samples.
Proper citation: MaryGold (RRID:SCR_000528) Copy
Software toolbox to facilitate quick and easy import, visualization and measurement for Event Related Potential (ERP) data. The toolbox can open and visualise ERP averaged data (Neuroscan, ascii formats), 2D/3D electrode coordinates and 3D cerebral tissue tesselations (meshes). All the features can be explored quickly and easily using the example data provided in the toolbox. The GUI interface is simple and intuitive.
Proper citation: Bioelectromagnetism Matlab Toolbox (RRID:SCR_006090) Copy
http://marsbar.sourceforge.net/
A toolbox for SPM which provides routines for region of interest analysis. Features include region of interest definition, combination of regions of interest with simple algebra, extraction of data for regions with and without SPM preprocessing (scaling, filtering), and statistical analyses of ROI data using the SPM statistics machinery.
Proper citation: MarsBaR region of interest toolbox for SPM (RRID:SCR_009605) Copy
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
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
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
http://sourceforge.net/projects/cnvhitseq/
A set of Java-based command-line tools for detecting Copy Number Variants (CNVs) using next-generation sequencing data.
Proper citation: cnvHiTSeq (RRID:SCR_013160) Copy
Ratings or validation data are available for this resource
http://broadinstitute.github.io/picard/
Java toolset for working with next generation sequencing data in the BAM format.
Proper citation: Picard (RRID:SCR_006525) Copy
http://bowtie-bio.sourceforge.net/recount/
RNA-seq gene count datasets built using the raw data from 18 different studies. The raw sequencing data (.fastq files) were processed with Myrna to obtain tables of counts for each gene. For ease of statistical analysis, they combined each count table with sample phenotype data to form an R object of class ExpressionSet. The count tables, ExpressionSets, and phenotype tables are ready to use and freely available. By taking care of several preprocessing steps and combining many datasets into one easily-accessible website, we make finding and analyzing RNA-seq data considerably more straightforward.
Proper citation: ReCount - A multi-experiment resource of analysis-ready RNA-seq gene count datasets (RRID:SCR_001774) Copy
http://genevenn.sourceforge.net/
A web application creating Venn diagrams from two or three gene lists.
Proper citation: GeneVenn (RRID:SCR_012117) Copy
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