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http://sourceforge.net/projects/vdjfasta/?source=navbar

Bioinformatics Perl extension for the analysis of antibody variable domain repertoires.

Proper citation: VDJFasta (RRID:SCR_013069) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/vcake/

A genetic sequence assembler capable of assembling millions of small nucleotide reads even in the presence of sequencing error.

Proper citation: VCAKE (RRID:SCR_013060) Copy   

•   Source: SciCrunch Registry

http://derisilab.ucsf.edu/software/price/index.html

Software for a de novo genome assembler implemented in C++.

Proper citation: PRICE (RRID:SCR_013063) Copy   

•   Source: SciCrunch Registry

http://www.nhlbi.nih.gov/about/dld/

Supports research on the causes, diagnosis, prevention, and treatment of lung diseases and sleep disorders. Research is funded through investigator-initiated and Institute-initiated grant programs and through contract programs in areas including asthma, bronchopulmonary dysplasia, chronic obstructive pulmonary disease, cystic fibrosis, respiratory neurobiology, sleep-disordered breathing, critical care and acute lung injury, developmental biology and pediatric pulmonary diseases, immunologic and fibrotic pulmonary disease, rare lung disorders, pulmonary vascular disease, and pulmonary complications of AIDS and tuberculosis. The Division is responsible for monitoring the latest research developments in the extramural scientific community as well as identifying research gaps and needs, obtaining advice from experts in the field, and implementing programs to address new opportunities. The DLD has three branches, the Airway Biology and Disease Branch, the Lung Biology and Disease Branch, and the National Center on Sleep Disorders Research.

Proper citation: NHLBI Division of Lung Diseases (RRID:SCR_013074) Copy   

•   Source: SciCrunch Registry

https://confluence.crbs.ucsd.edu/display/NIF/OntoQuestMain

An ontology management module to perform ontology-based search over data sources. This management system permits a user to store, search and navigate any number of OWL-structured ontologies. Ontoquest may also be accessed through a variety of web services via the Neuroscience Information Framework.

Proper citation: OntoQuest (RRID:SCR_013281) Copy   

•   Source: SciCrunch Registry

http://www.aans.org/

The American Association of Neurological Surgeons is dedicated to advancing the specialty of neurological surgery and serving as the spokes organization for all practitioners of the specialty of neurosurgery, in order to provide the highest quality of care to our patients. :Founded in 1931 as the Harvey Cushing Society, the American Association of Neurological Surgeons (AANS) is a scientific and educational association with over 7,400 members worldwide. The AANS is dedicated to advancing the specialty of neurological surgery in order to provide the highest quality of neurosurgical care to the public. All Active members of the AANS are board certified by the American Board of Neurological Surgery, the Royal College of Physicians and Surgeons of Canada, or the Mexican Council of Neurological Surgery, A.C. Neurosurgery is the medical specialty concerned with the prevention, diagnosis, treatment and rehabilitation of disorders that affect the spinal column, spinal cord, brain, nervous system and peripheral nerves. For more information on what neurosurgeons do, visit our public pages at : :www.NeurosurgeryToday.org : : :. Visitors to our Web site can find Member Counts under membership including demographic details.

Proper citation: American Association of Neurological Surgeons (RRID:SCR_013209) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages//2.10/bioc/html/HiTC.html

Software package to explore high-throughput ''C'' data such as 5C or Hi-C.

Proper citation: HiTC (RRID:SCR_013175) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/conifer/

Uses exome sequencing data to find copy number variants (CNVs) and genotype the copy-number of duplicated genes.

Proper citation: CoNIFER (RRID:SCR_013213) Copy   

•   Source: SciCrunch Registry

http://rdxplorer.sourceforge.net/

A computational tool for copy number variants (CNV) detection in whole human genome sequence data using read depth (RD) coverage.

Proper citation: RDXplorer (RRID:SCR_013290) Copy   

•   Source: SciCrunch Registry

http://waprna.big.ac.cn/

A free web-based application for the processing of high-throughput RNA-Seq data from next generation sequencing (NGS) platforms, such as Genome Analyzer of Illumina Inc. (Solexa) and SOLiD of Applied Biosystems (SOLiD).

Proper citation: wapRNA (RRID:SCR_013292) Copy   

•   Source: SciCrunch Registry

http://www.diogenes-eu.org

Diogenes is a pan-European Programme targeting the obesity problem from a dietary perspective: seeking new insights and new routes to prevention. An Integrated Project of the EU Sixth Framework Programme for Research and Technological Development (2005-2009). A new methodology has been developed for consistent assignment of GI values to foods across the five European databases used in the Diogenes intervention study. GI values have been assigned according to five decreasing levels of confidence: (1) Measured values for specific foods; (2) Published values from published sources; (3) Equivalent values where published values for similar foods existed; (4) Estimated values three values selected representing low/medium/high GI ranges; (5) Nominal values assigned as 70, where no other value could be assigned with sufficient confidence. Sponsor. A a r h u s K a r l s h a m n D e n m a r k A / S Products: Vegetable Oils (Maize and Rapeseed) click here for the link to the website of AarhusKarlshamn Denmark B a r i l l a Products: Pasta click here for the link to the website of Barilla B e a u v a i s Products: Canned fish products, jam, soups & convenience foods click here for the link to the website of Beauvais C a m p i n a I n s t i t u t e At the Campina Institute dairy products and science come together. The Campina brands include among others: Optimel/ Optiwel, Vifit, Milner, Valess Click here for the link to the website of Campina Institute C o c a - C o l a S e r v i c e s S . A . Products: beverages click here for the link to the website of Coca-Cola Services S.A. D a l o o n Products: Spring rolls and other convenience foods click here for the link to the website of Daloon D a n g S / A Products: egg products click here for the link to the website of Dang A/S D a n i s c o Products: Sugar (different types) click here for the link to the website of Danisco D a n i s h D a i r y B o a r d Products: Dairy products (milk, yoghurt, cheese) click here for the link to the website of the Danish Dairy Board D a n s k e S l a g t e r i e r Products: Pig Meat Products (various types) click here for the link to the website of Danske Slagterier D r . O e t k e r Products: Ready meals click here for the link to the website of Dr. Oetker E u r o g r a n A / S Products: Instant chocolate, cappuccino, soup and mashed poptatoes click here for the link to the website of Eurogran A/S F r i g o d a n Products: Frozen vegetables click here for the link to the website of Frigodan F r i s k o Products: Ice cream click here for the link to the website of Frisko G a m b a F o o d Products: Frozen fish (different types of European and Asian origin) G i l d e N o r g e B A Products: meat click here for the link to the website of Gilde Norge BA H a t t i n g Products: Bread products (different types) click here for the link to the website of Hatting H e i n z Products: ketchup and a broad range of products under HONIG, Konininklijke de Ruijter, VENZ, Carvan Cevitan, Roosvicee click here for the link to the website of Heinz H j e r t i n g L a k s Products: salmon products click here for the link to the website of Hjerting Laks K e l l o g g '' s D e n m a r k Products: different types of Breakfast Cereals Click here for the link to the website of Kellogg''s Denmark K e l l o g g '' s E u r o p e Products: Ready-To-Eat Cereals and Cereal Bars Click here for the link to the website of Kellogg''s K d b r a n c h e n s F l l e s r d Products: meat: beaf and veal click here for the link to the website of Kdbranchens Fllesrd K r a f t Products: chocolate, Philadelphia cream cheese, pasta, Estrella chips & nuts, mayonaise, salad dressings click here for the link to the website of Kraft L a n t m n n e n M i l l s A / S Products: various grains and flour L U , G e n e r a l B i s c u i t s N e d e r l a n d B . V . Products: biscuits click here for the link to the website of LU L y k k e b e r g A / S Products: Fish (marinated herring) click here for the link to the website of Lykkeberg A/S M a s t e r f o o d s Products: Rice and confectionery click here for the different websites of Masterfoods: Uncle Bens, Mars, Twix, Snickers, M&M''s, Masterfoods N u t r i t i o n e t S a n t / M o d i f a s t Products: Modifast (Low Calorie Diet) click here for the link to the website of Nutrition et Sant click here for the link to the website of Modifast P a r t n e r s h i p f o r D a n i s h P o t a t o e s Products: potatoes (different varieties) click here for the link to the website of the Partnership for Danish Potatoes P a s t a l i f e Products: pasta (with high protein content) click here for the link to the website of Pastalife R a h b e k Products: Frozen, ready-made fish dishes click here for the link to the website of Rahbek R i e b e r & S n D a n m a r k A / S Products: mustard, ketchup, mayonnaise, sanwich filling, spreads and other dressings click on the following links for the different websites of Rieber and Sn Danmark A/S: Rieberson, Bahncke, K-Salat R o y a l G r e e n l a n d A / S Products: cold-water prawns click here for the link to the website of Royal Greenlands A/S S c h u l s t a d Products: Rye bread and wheat bread, including high- and low GI varieties click here for the link to the website of Schulstad S n d e r j y d s k K l Products: Frozen kale, spinach and cabbage. click here for the link to the website of Snderjydsk Kl S u i k e r U n i e Products: different types of sugar click here for the link to the website of Suiker Unie T u l i p F o o d C o m p a n y Products: Meat products (cold cuts, cooked meat, bacon, meat balls, ready-meals, soups etc.) Click here for the link to the website of Tulip Food Company U n i l e v e r Products: a broad range of products under Becel, Bertolli, Calv, Knorr, Iglo, Mora, Conimex, Unox click here for the link to the website of Unilever W a s a b r d A / S Products: Crisp bread click on the following links for the different websites of Wasabrd A/S: Wasa Denmark or Wasa International

Proper citation: Diogenes (RRID:SCR_013293) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/pia2/

A prefix indexing and alignment software for next-generation sequencing (NGS) for whole human genome.

Proper citation: PIA (RRID:SCR_013267) Copy   

•   Source: SciCrunch Registry

https://github.com/lh3/wgsim

A small tool for simulating sequence reads from a reference genome.

Proper citation: Wgsim (RRID:SCR_013269) Copy   

•   Source: SciCrunch Registry

http://tripod.nih.gov/

Tripod is a user-friendly chemical genomics browser that is currently being developed by the informatics group at the NIH Chemical Genomics Center. The main goal of Tripod is to facilitate easy access to chemical and biological data in an intuitive, user-friendly tool. To this end, the development of Tripod is inspired by the ubiquitous iTunes software, whereby browsing and managing of media contents are being adapted to chemical and biological data.

Proper citation: Tripod (RRID:SCR_013147) Copy   

•   Source: SciCrunch Registry

http://soap.genomics.org.cn/SOAPdenovo-Trans.html

A de novo transcriptome assembler basing on the SOAPdenovo framework, adapt to alternative splicing and different expression level among transcripts., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: SOAPdenovo-Trans (RRID:SCR_013268) Copy   

•   Source: SciCrunch Registry

http://compbio.cs.ucr.edu/brat/

BRAT is an accurate and efficient tool for mapping short bisulfite-treated reads obtained from the Solexa-Illumina Genome Analyzer.

Proper citation: BRAT (RRID:SCR_013159) Copy   

•   Source: SciCrunch Registry

http://alumni.cs.ucr.edu/~liw/cem.html

An algorithm to assemble transcripts and estimate their expression levels from RNA-Seq reads.

Proper citation: CEM (RRID:SCR_013241) Copy   

•   Source: SciCrunch Registry

http://qccpack.sourceforge.net

QccPack provides an open-source collection of library routines and utility programs for quantization, compression, and coding of data. QccPack has been written to provide very flexible and general implementations of procedures commonly used in coding and compression applications. QccPack is intended for use in the development of prototypes of coding and compression systems, and in academic research. QccPack includes routines for entropy coding, scalar quantization, vector quantization, and wavelet transforms. Additonally, an open-source implementation of SPIHT is available as an optional module. QccPack provides an open-source collection of library routines and utility programs for quantization, compression, and coding of data. QccPack has been written to provide very flexible and general implementations of procedures commonly used in coding and compression applications. The essential component of the QccPack collection is a library (a static library, libQccPack.a, and, if supported on your system, a dynamic library, libQccPack.so) of procedures implementing a large variety of compression and coding algorithms. Application programs may make use of the QccPack library routines by linking the application against the library during compilation. Each library function is very general in its implementation so to be useful in a large variety of applications. Additionally, much of the functionality of the library routines has been provided in the form of stand-alone executable programs. Probably the prime importance of these utility programs is that they provide examples of how to interface with many of the QccPack library routines. The utility programs could also be called from scripts to simulate the operation of complex coding and compression systems before implementing all the system functionality into one stand-alone program. Currently, QccPack consists of over 55,000 lines of C code implementing over 500 library routines and over 50 stand-alone utility programs. The major functionalities currently implemented include: * Entropy coding o Arithmetic coding including multiple-context adaptive and nonadaptive models o Huffman coding o Golomb and adaptive Golomb coding * Scalar Quantization (SQ) o Uniform SQ o Dead-zone SQ o -law and A-law SQ o Lloyd algorithm for optimal SQ design * Vector quantization (VQ) o Generalized Lloyd algorithm (GLA) for VQ-codebook design o Full-search VQ encoding and decoding o Entropy-constrained-VQ (ECVQ) training, encoding, and decoding o Multistage VQ (MSVQ) (also called residual VQ (RVQ)) training, encoding, and decoding * Adaptive vector quantization (AVQ) o The generalized-threshold-replenishment (GTR) algorithm o The Paul algorithm o Gersho-Yano algorithm o Coding of side information * Wavelet transforms, wavelet-based subband coding o Discrete wavelet transform (DWT) using first-generation filter banks and popular orthonormal and biorthogonal wavelets o Lifting implementations of DWT for popular wavelets o Two-dimensional DWT in the form of dyadic subband pyramids o Three-dimensional DWT in the form of dyadic subband pyramids as well as a packet transform o Shape-adaptive DWT (SA-DWT) for 1D and 2D signals o Redundant DWT (RDWT), aka, the algorithme trous o The SR algorithm for wavelet-based image coding o The SFQ algorithm for wavelet-based image coding o The WDR algorithm for wavelet-based image coding o The 3D-WDR algorithm for wavelet-based image-cube coding o The tarp-filter algorithm for wavelet-based image coding o The 3D-tarp algorithm for wavelet-based image-cube coding o The TCE algorithm for wavelet-based image coding o The BISK algorithm for wavelet-based shape-adaptive image coding o The 3D-BISK algorithm for wavelet-based image-cube coding * Error-correcting codes o Field arithmetic, including Gaussian-elimination matrix inversion o Reed-Solomon encoding and decoding o CRC codes o Trellis codes o Hard and soft Viterbi decoding * Image processing o Routines for reading and writing gray and color still images and sequences of images (via PGM and PPM formats) o Routines for reading and writing 3D image-cube volumes o Image and image-sequence deinterlacing o Image differential-pulse-code modulation (DPCM) o Color-space conversions: RGB, YUV, CIE XYZ, CIE UCS, CIE modified UCS o Block-based DCT and inverse DCT * Video coding o The spatial-block algorithm for image-sequence coding o The RDWT-block algorithm for image-sequence coding o The RWMH algorithm for image-sequence coding o Block-based motion estimation and motion compensation o Motion estimation and motion compensation using regular triangle meshes o Encoding and decoding of motion-vector fields * General routines o Vector math (up/down sampling, sorting, dot product, addition/subtraction, etc.) o Matrix math (addition/subtraction, vector-matrix multiplication, etc.) o Linked lists and associated operations o Entropy estimation (first and second order) o General file input and output, including automatic detection and reading/writing of gzip-compressed files o Character bit-packing for binary bitstream input/output o Memory-based fifo for binary bitstreams o Conversion between various file formats used by library routines o Error-message tracking, formatting, and output o Automatic command-line parameter parsing In addition to the standard functionalities listed above, there exist optional modules that can be added to the QccPack library. Usually, these modules are available under licensing terms different from the GPL/LGPL licenses of QccPack and may contain patented algorithms; refer to the documentation included with each module for specific details. These modules are downloaded separately from QccPack and are not enabled by default during the building of QccPack. The currently available optional modules and their functionalities are: * QccPackSPIHT o The Set Partitioning in Hierarchical Trees (SPIHT) algorithm for wavelet-based image coding * QccPackSPECK o The Set-Partitioning Embedded Block (SPECK) algorithm for wavelet-based image coding Abstract: We describe the QccPack software package, an open-source collection of library routines and utility programs for quantization, compression, and coding of data. QccPack is being written to expedite data-compression research and development by providing general and reliable implementations of common compression techniques. Functionality of the current release includes entropy coding, scalar quantization, vector quantization, adaptive vector quantization, wavelet transforms and subband coding, error-correcting codes, image-processing support, and general vector-math, matrix-math, file-I/O, and error-message routines. All QccPack functionality is accessible via library calls; additionally, many utility programs provide command-line access. The QccPack software package, downloadable free of charge from the QccPack Web page, is published under the terms of the GNU General Public License and the GNU Library General Public License which guarantee source-code access and as well as allow redistribution and modification. Additionally, there exist optional modules that implement certain patented algorithms. These modules are downloadable separately and are typically issued under licenses that permit only non-commercial use. This material is based upon work supported in part by the National Science Foundation under Grant No. INT-9600260.

Proper citation: QccPack (RRID:SCR_013240) Copy   

•   Source: SciCrunch Registry

http://bioinfo.au.tsinghua.edu.cn/seqsite/

Software for detecting transcription factor binding sites from ChIP-seq data.

Proper citation: SeqSite (RRID:SCR_013243) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/2.9/bioc/html/Repitools.html

Software tools for the analysis of enrichment-based epigenomic data.

Proper citation: Repitools (RRID:SCR_013242) Copy   

•   Source: SciCrunch Registry