SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
Debian is Linux distribution composed of free and open source software, developed by community supported Debian Project, which was established by Ian Murdock on August 16, 1993.Debian comes with over 59000 packages (precompiled software that is bundled up in nice format for easy installation on your machine), package manager (APT), and other utilities that make it possible to manage thousands of packages on thousands of computers as easily as installing single application.
Proper citation: Debian (RRID:SCR_006638) Copy
Ratings or validation data are available for this resource
Collection based on a collaborative effort of popular neuroscience research software for the Debian operating system as well as Ubuntu and other derivatives. Popular packages include AFNI, FSL, PyMVPA and many others. It contains both unofficial or prospective packages which are not (yet) available from the main Debian archive, as well as backported or simply rebuilt packages also available elsewhere. A listing of current and planned projects is available if you want to get involved. The main goal of the project is to provide a versatile and convenient environment for neuroscientific research that is based on open-source software. To this end, the project offers a package repository that complements the main Debian (and Ubuntu) archive. NeuroDebian is not yet another Linux distribution, but rather an effort inside the Debian project itself. Software packages are fully integrated into the Debian system and from there will eventually migrate into Ubuntu as well. With NeuroDebian, installing and updating neuroscience software is no different from any other part of the operating system. Maintaining a research software environment becomes as easy as installing an editor. There is also virtual machine to test NeuroDebian on Windows or Mac OS. If you want to see your software packaged for Debian, please drop them a note.
Proper citation: neurodebian (RRID:SCR_004401) Copy
Alignment software for large-scale protein contact or protein-protein interaction prediction optimized for speed through shorter runtimes. FreeContact provides the opportunity to compute contact predictions in any environment (desktop or cloud).
Proper citation: FreeContact (RRID:SCR_016113) Copy
https://github.com/GregoryFaust/samblaster
Software tool to mark duplicates and extract discordant and split reads from SAM files. This fast and flexible program for marking duplicates in read-id grouped paired-end SAM files can also optionally output discordant read pairs and/or split read mappings to separate SAM files, and/or unmapped/clipped reads to a separate FASTQ file. When marking duplicates, samblaster will require approximately 20MB of memory per 1M read pairs.
Proper citation: SAMBLASTER (RRID:SCR_000468) Copy
An efficient software tool for the local alignment of pyrosequencing reads produced by the GS FLX (454) Genome Analyzer technology against a reference genome sequence. The approach explores the characteristics of the data in re-sequencing applications and uses state of the art BWT-based indexing techniques combined with a flexible seed-based approach, leading to a fast and accurate algorithm which needs very little user parameterization. Although initially developed having this specific technology in mind, this software performs equally well on any other platform that can return its sequencing reads in the FASTA, FASTQ or SFF formats, including Illumina, Ion Torrent and Pacific Biosciences technologies.
Proper citation: TAPyR (RRID:SCR_000588) Copy
http://mendel.stanford.edu/SidowLab/downloads/gerp/
Software that identifies constrained elements in multiple alignments by quantifying substitution deficits. These deficits represent substitutions that would have occurred if the element were neutral DNA, but did not occur because the element has been under functional constraint. We refer to these deficits as Rejected Substitutions. Rejected substitutions are a natural measure of constraint that reflects the strength of past purifying selection on the element. GERP estimates constraint for each alignment column; elements are identified as excess aggregations of constrained columns. A false-positive rate (which is user-settable) is calculated using "shuffled" alignments in which the order of columns is randomized.
Proper citation: GERP (RRID:SCR_000563) Copy
http://www.broadinstitute.org/cancer/cga/mutect
Software for the reliable and accurate identification of somatic point mutations in next generation sequencing data of cancer genomes.
Proper citation: MuTect (RRID:SCR_000559) Copy
http://sourceforge.net/projects/srma/
A post-alignment micro re-aligner for next-generation high throughput sequencing data.
Proper citation: SRMA (RRID:SCR_000669) Copy
http://sourceforge.net/projects/cuda-ec/
A fast parallel error correction tool for short reads.
Proper citation: CUDA-EC (RRID:SCR_001090) Copy
A high-performance visualization tool for interactive exploration of large, integrated genomic datasets written primarily in JavaScript. It supports a wide variety of data types, including array-based and next-generation sequence data, and genomic annotations.
Proper citation: JBrowse (RRID:SCR_001004) Copy
http://131.174.198.125/bioinfo/gimmemotifs/
Software that provides a de novo motif prediction pipeline, especially suited for ChIP-seq datasets. It incorporates several existing motif prediction algorithms in an ensemble method to predict motifs and clusters these motifs using the WIC similarity scoring metric.
Proper citation: GimmeMotifs (RRID:SCR_001146) Copy
http://www.bioconductor.org/packages/release/bioc/html/rbsurv.html
Software package that selects genes associated with survival.
Proper citation: rbsurv (RRID:SCR_001175) Copy
http://www.bioinformatics.babraham.ac.uk/projects/sherman/
Software tool to simulate FastQ files for high-throughput sequencing experiments. It allows the user to introduce various "contaminants" into the sequences, such as basecall errors, SNPs, adapter fragments etc., in order to evaluate the influence of common problems observed in many Next-Gen Sequencing experiments.
Proper citation: Sherman (RRID:SCR_001294) Copy
https://code.google.com/p/ibm-cbc-genomic-tools/
A flexible computational platform, comprising both a command-line set of tools and a C++ API, for the analysis and manipulation of high-throughput sequencing data such as DNA-seq, RNA-seq, ChIP-seq and MethylC-seq. It implements a variety of mathematical operations between sets of genomic regions thereby enabling the prototyping of computational pipelines that can address tasks from preprocessing and quality control to meta-analyses. The user can create average read profiles across transcriptional start sites or enhancer sites, quickly prototype customized peak discovery methods for ChIP-seq experiments, perform genome-wide statistical tests such as enrichment analyses, design controls via appropriate randomization schemes, among other applications. In addition to enabling rapid prototyping, the platform is designed to analyze large-datasets in a single-pass fashion in order to minimize memory and intermediate file requirements. The platform supports the widely used BED format to facilitate visualization as well as integration with existing platforms and pipelines such as Galaxy or BioConductor.
Proper citation: GenomicTools (RRID:SCR_001205) Copy
http://www.genome.duke.edu/labs/ohler/research/PARalyzer/
Software tool to generate a high resolution map of interaction sites between RNA-binding proteins and their targets. The algorithm utilizes the deep sequencing reads generated by the newly developed PAR-CLIP (Photoactivatable-Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation) protocol. The use of photoactivatable nucleotides in the PAR-CLIP protocol results in a more efficient crosslinking between the RNA-binding protein and its target relative to other CLIP methods; in addition a nucleotide substitution occurs at the site of crosslinking during Illumina library preparation. PARalyzer utilizes this nucleotide substition in a kernel density estimate classifier to generate the high resolution set of Protein-RNA interaction sites.
Proper citation: PARalyzer (RRID:SCR_001208) Copy
http://yiplab.cse.cuhk.edu.hk/probrna/
Software for computational identification of protein binding sites on RNAs using high-throughput RNA structure-probing data.
Proper citation: ProbRNA (RRID:SCR_001288) Copy
Software to classify the function and phylogeny of reads as short as 30 bp. It is flexible, which can utilize multiple data modules and downstream analysis scripts. It is fast, reading in signature lists of 5-500 million peptide signatures in 1-15 minutes, and subsequently processes genomic fragments at the rate of 6 Gbp/hr. It parallelizes without significant increase in memory requirements until I/O bound on multiple input files; parallelization works well on 64 processors.
Proper citation: Sequedex (RRID:SCR_001233) Copy
http://www.bioinformatics.org/peakanalyzer/wiki/
A set of standalone software programs for the automated processing of any genomic loci, with an emphasis on datasets consisting of ChIP-derived signal peaks. The software is able to identify individual binding / modification sites from enrichment loci, retrieve peak region sequences for motif discovery, and integrate experimental data with different classes of annotated elements throughout the genome. PeakAnalyzer requires a peak file and a feature annotation file in BED or GTF format. Complete annotation files for the current builds of the human (HG19) and mouse (MM9) genomes are provided with the software distribution.
Proper citation: PeakAnalyzer (RRID:SCR_001194) Copy
http://sv.gersteinlab.org/breakseq/
Software for scanning reads from short-read sequenced genomes against a human breakpoint library to accurately identify structural variants (SVs). The library of breakpoints at nucleotide resolution were assembled from collating and standardizing ~2,000 published structural variants (SVs). For each breakpoint, its ancestral state (through comparison to primate genomes) was inferred and its mechanism of formation (e.g., nonallelic homologous recombination, NAHR).
Proper citation: BreakSeq (RRID:SCR_001186) Copy
http://www-genepi.med.utah.edu/suppl/SLOPE/index.html
Software that consists of two command-line utilities, slope_align (which finds the best split-read alignments to the reference genome) and slope_cluster (which clusters and outputs the alignments).
Proper citation: SLOPE (RRID:SCR_001185) Copy
Can't find your Tool?
We recommend that you click next to the search bar to check some helpful tips on searches and refine your search firstly. Alternatively, please register your tool with the SciCrunch Registry by adding a little information to a web form, logging in will enable users to create a provisional RRID, but it not required to submit.
Welcome to the FDI Lab - SciCrunch.org Resources search. From here you can search through a compilation of resources used by FDI Lab - SciCrunch.org and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that FDI Lab - SciCrunch.org has compiled. You can navigate through those categories from here or change to a different tab to execute your search through. Each tab gives a different perspective on data.
If you have an account on FDI Lab - SciCrunch.org then you can log in from here to get additional features in FDI Lab - SciCrunch.org such as Collections, Saved Searches, and managing Resources.
Here is the search term that is being executed, you can type in anything you want to search for. Some tips to help searching:
You can save any searches you perform for quick access to later from here.
We recognized your search term and included synonyms and inferred terms along side your term to help get the data you are looking for.
If you are logged into FDI Lab - SciCrunch.org you can add data records to your collections to create custom spreadsheets across multiple sources of data.
Here are the sources that were queried against in your search that you can investigate further.
Here are the categories present within FDI Lab - SciCrunch.org that you can filter your data on
Here are the subcategories present within this category that you can filter your data on
If you have any further questions please check out our FAQs Page to ask questions and see our tutorials. Click this button to view this tutorial again.