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https://code.google.com/p/discovering-cse/
Software for discovering motifs that induce sequencing errors.
Proper citation: discovering-cse (RRID:SCR_011832) Copy
https://sites.google.com/site/moleculetagtoolbox/
A software package for building accurate ConSeqs from tagged reads.
Proper citation: MT-Toolbox (RRID:SCR_011833) Copy
http://ftp://ftp.pasteur.fr/pub/gensoft/projects/AlienTrimmer/
Allows detecting and removing multiple alien sequences in both ends of sequence reads.
Proper citation: AlienTrimmer (RRID:SCR_011835) Copy
http://hiv.sanbi.ac.za/software/qtrim
A next generation sequence quality trimming tool.
Proper citation: QTrim (RRID:SCR_011842) Copy
https://github.com/najoshi/sabre
Software tool to demultiplex barcoded reads into separate files. Works on both single-end and paired-end data in fastq format. Used in next generation sequencing to analyze a broad range of data.
Proper citation: sabre (RRID:SCR_011843) Copy
https://github.com/vsbuffalo/scythe
Scythe uses a Naive Bayesian approach to classify contaminant substrings in sequence reads.
Proper citation: Scythe (RRID:SCR_011844) Copy
http://www.scbi.uma.es/ingebiol/session/new/seqtrimnext
A customizable and distributed pre-processing software for NGS (Next Generation Sequencing) biological data.The old version for Sanger sequences, Seqtrim, has been discontinued.
Proper citation: SeqtrimNEXT (RRID:SCR_011845) Copy
http://genome.ufl.edu/rivalab/pasta/
A complete pipeline for the analysis of alternative splicing using RNA-Sequencing data.
Proper citation: PASTA (RRID:SCR_008770) Copy
http://www.raetschlab.org/suppl/qpalma
An alignment tool targeted to align spliced reads produced by Next Generation sequencing platforms such as Illumina Solexa or 454.
Proper citation: QPALMA (RRID:SCR_008791) Copy
http://r-forge.r-project.org/projects/sequgio/
An algorithm to estimate isoforms expression from RNA-seq data based on a model that doesn''t assume uniform distribution of count within transcripts.
Proper citation: Sequgio (RRID:SCR_008867) Copy
http://lrcv-crp-sante.s3-website-us-east-1.amazonaws.com/
A gene set analysis algorithm for biomarker identification in the cloud.
Proper citation: YunBe (RRID:SCR_008740) Copy
An information extracting and processing package for biological literature that can be used online or installed locally via a downloadable software package, http://www.textpresso.org/downloads.html Textpresso's two major elements are (1) access to full text, so that entire articles can be searched, and (2) introduction of categories of biological concepts and classes that relate two objects (e.g., association, regulation, etc.) or describe one (e.g., methods, etc). A search engine enables the user to search for one or a combination of these categories and/or keywords within an entire literature. The Textpresso project serves the biological and biomedical research community by providing: * Full text literature searches of model organism research and subject-specific articles at individual sites. Major elements of these search engines are (1) access to full text, so that the entire content of articles can be searched, and (2) search capabilities using categories of biological concepts and classes that relate two objects (e.g., association, regulation, etc.) or identify one (e.g., cell, gene, allele, etc). The search engines are flexible, enabling users to query the entire literature using keywords, one or more categories or a combination of keywords and categories. * Text classification and mining of biomedical literature for database curation. They help database curators to identify and extract biological entities and facts from the full text of research articles. Examples of entity identification and extraction include new allele and gene names and human disease gene orthologs; examples of fact identification and extraction include sentence retrieval for curating gene-gene regulation, Gene Ontology (GO) cellular components and GO molecular function annotations. In addition they classify papers according to curation needs. They employ a variety of methods such as hidden Markov models, support vector machines, conditional random fields and pattern matches. Our collaborators include WormBase, FlyBase, SGD, TAIR, dictyBase and the Neuroscience Information Framework. They are looking forward to collaborating with more model organism databases and projects. * Linking biological entities in PDF and online journal articles to online databases. They have established a journal article mark-up pipeline that links select content of Genetics journal articles to model organism databases such as WormBase and SGD. The entity markup pipeline links over nine classes of objects including genes, proteins, alleles, phenotypes, and anatomical terms to the appropriate page at each database. The first article published with online and PDF-embedded hyperlinks to WormBase appeared in the September 2009 issue of Genetics. As of January 2011, we have processed around 70 articles, to be continued indefinitely. Extension of this pipeline to other journals and model organism databases is planned. Textpresso is useful as a search engine for researchers as well as a curation tool. It was developed as a part of WormBase and is used extensively by C. elegans curators. Textpresso has currently been implemented for 24 different literatures, among them Neuroscience, and can readily be extended to other corpora of text.
Proper citation: Textpresso (RRID:SCR_008737) Copy
http://bioinformatics.fccc.edu/software/OpenSource/FGDP/FGDP.shtml
A Java-based, Microarray or Genechip data analysis system.
Proper citation: FGDP (RRID:SCR_008910) Copy
http://www.biomedcentral.com/1471-2105/14/357/abstract
Sample size calculation based on exact test for assessing differential expression analysis in RNA-seq data. R code is available from the corresponding author.
Proper citation: A sample size calculation method (RRID:SCR_009469) Copy
http://www.cibiv.at/~niko/ngc/
A compressor for aligned HTS sequencing data that enables the complete lossless and lossy compression of mapped alignment data stored in SAM/BAM files.
Proper citation: NGC (RRID:SCR_009342) Copy
http://geckoe.sourceforge.net/
A complete, high-capacity centralized gene expression analysis system, developed in response to the needs of a distributed user community.
Proper citation: Gecko (RRID:SCR_009001) Copy
http://homes.cs.washington.edu/~dcjones/quip/
Compresses next-generation sequencing data in the FASTQ and SAM/BAM formats with extreme prejudice.
Proper citation: Quip (RRID:SCR_009362) Copy
http://bioinformatics.ua.pt/software/mfcompress/
A compression tool for FASTA and multi-FASTA files.
Proper citation: MFCompress (RRID:SCR_009301) Copy
http://bioinformatics.research.nicta.com.au/software/rlz/
Optimized relative Lempel-Ziv compression of genomes.
Proper citation: RLZ (RRID:SCR_009420) Copy
http://ftp://ftp.ieeta.pt/~ap/codecs/GReEn1.tar.gz
A compression tool recently proposed for compressing genome resequencing data using a reference genome sequence., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: GReEn (RRID:SCR_009264) Copy
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Welcome to the Neuroscience Information Framework Project, designed to serve the biomedical research community. NIF maintains the largest searchable collection of neuroscience data, the largest catalog of biomedical resources, and the largest ontology for neuroscience on the web. We welcome all feedback and suggestions and are actively looking for resource providers to make their resources accessible through NIF. Learn about the tools available to help you share your data and discover a dynamic inventory of Web-based neuroscience resources.
