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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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SOAPdenovo-Trans Resource Report Resource Website 100+ mentions |
SOAPdenovo-Trans (RRID:SCR_013268) | SOAPdenovo-Trans | software resource | 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. | is listed by: OMICtools | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01324 | SCR_013268 | 2026-07-25 12:07:51 | 170 | |||||||||
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BRAT Resource Report Resource Website 50+ mentions |
BRAT (RRID:SCR_013159) | BRAT | software resource | BRAT is an accurate and efficient tool for mapping short bisulfite-treated reads obtained from the Solexa-Illumina Genome Analyzer. | is listed by: OMICtools | OMICS_00577 | SCR_013159 | Bisulfite-treated Reads Analysis Tool | 2026-07-25 12:07:44 | 53 | |||||||||
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CEM Resource Report Resource Website 1+ mentions |
CEM (RRID:SCR_013241) | CEM | software resource | An algorithm to assemble transcripts and estimate their expression levels from RNA-Seq reads. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of California at Riverside; California; USA |
OMICS_01271, biotools:cem | https://bio.tools/cem | SCR_013241 | CEM: Transcriptome Assembly and Isoform Expression Level Estimation from Biased RNA-Seq Reads | 2026-07-25 12:07:48 | 1 | |||||||
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QccPack Resource Report Resource Website 1+ mentions |
QccPack (RRID:SCR_013240) | software resource | 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. | nif-0000-31387 | SCR_013240 | QccPack | 2026-07-25 12:07:46 | 1 | |||||||||||
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SeqSite Resource Report Resource Website |
SeqSite (RRID:SCR_013243) | SeqSite | software resource | Software for detecting transcription factor binding sites from ChIP-seq data. | is listed by: OMICtools | OMICS_00493 | SCR_013243 | SeqSite: ChIP-Seq Binding Site Identification | 2026-07-25 12:07:46 | 0 | |||||||||
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Repitools Resource Report Resource Website 10+ mentions |
Repitools (RRID:SCR_013242) | Repitools | software resource | Software tools for the analysis of enrichment-based epigenomic data. |
is listed by: OMICtools has parent organization: Bioconductor |
OMICS_00619 | SCR_013242 | 2026-07-25 12:07:50 | 21 | ||||||||||
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SmashCommunity Resource Report Resource Website 1+ mentions |
SmashCommunity (RRID:SCR_013245) | SmashCommunity | software resource | A stand-alone metagenomic annotation and analysis pipeline suitable for data from Sanger and 454 sequencing technologies. |
is listed by: OMICtools has parent organization: EMBL - Bork Group |
OMICS_01482 | SCR_013245 | 2026-07-25 12:07:48 | 8 | ||||||||||
|
Entrez Utilities Resource Report Resource Website 10+ mentions |
Entrez Utilities (RRID:SCR_013249) | software resource |
Entrez Programming Utilities are tools that provide access to Entrez data outside of the regular web query interface and may be helpful for retrieving search results for future use in another environment. Additional information is available in the NCBI Bookshelf Short Courses Building Customized Data Pipelines Using the Entrez Programming Utilities (eUtils) and the NCBI PowerScripting course. User Requirements: Please read for important information on scripting NCBI servers. EInfo: Provides field index term counts, last update, and available links for each database. ESearch: Searches and retrieves primary IDs (for use in EFetch, ELink, and ESummary) and term translations and optionally retains results for future use in the user''s environment. EPost: Posts a file containing a list of primary IDs for future use in the user''s environment to use with subsequent search strategies. ESummary: Retrieves document summaries from a list of primary IDs or from the user''s environment. EFetch: Retrieves records in the requested format from a list of one or more primary IDs or from the user''s environment. ELink: Checks for the existence of an external or Related Articles link from a list of one or more primary IDs. Retrieves primary IDs and relevancy scores for links to Entrez databases or Related Articles; creates a hyperlink to the primary LinkOut provider for a specific ID and database, or lists LinkOut URLs and Attributes for multiple IDs. EGQuery: Provides Entrez database counts in XML for a single search using Global Query. ESpell: Retrieves spelling suggestions. SOAP Interface for Entrez Utilities PMID to PMC ID Converter Entrez DTDs Demonstration Program Announcement Mailing List Leasing Data from the National Library of Medicine Help Desk User Requirements Do not overload NCBI''s systems. Users intending to send numerous queries and/or retrieve large numbers of records from Entrez should comply with the following: Run retrieval scripts on weekends or between 9 pm and 5 am Eastern Time weekdays for any series of more than 100 requests. Send E-utilities requests to http://eutils.ncbi.nlm.nih.gov, not the standard NCBI Web address. Make no more than 3 requests every 1 second. Use the URL parameter email, and tool for distributed software, so that we can track your project and contact you if there is a problem. NCBI''s Disclaimer and Copyright notice must be evident to users of your service. NLM does not claim the copyright on the abstracts in PubMed; however, journal publishers or authors may. NLM provides no legal advice concerning distribution of copyrighted materials, consult your legal counsel. |
has parent organization: National Library of Medicine | nif-0000-30519 | http://eutils.ncbi.nlm.nih.gov/entrez/query/static/eutils_help.html | SCR_013249 | Entrez Utilities | 2026-07-25 12:07:46 | 21 | |||||||||
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BrainVisa Morphology extensions Resource Report Resource Website 1+ mentions |
BrainVisa Morphology extensions (RRID:SCR_013248) | BrainVisa Morphology extensions | software resource | An extension projects providing computational tools for performing regional morphological measurements to assess groupwise differences and track morphological changes during maturation and aging. The extensions include computation of regional GM thickness, 3D gyrification index, sulcal lenght and depth and sulcal span. These tools are distributed in the form of plugins for a popular analysis package BrainVisa | analyze, c++, image display, linux, macos, microsoft, morphology, magnetic resonance, nifti, posix/unix-like, quantification, shape analysis, software, visualization, windows |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: BrainVISA / Anatomist is related to: INCF Software Center |
Artistic License | nlx_155716 | http://www.nitrc.org/projects/brainvisa_ext | SCR_013248 | 2026-07-25 12:07:50 | 1 | |||||||
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miRSeqNovel Resource Report Resource Website 1+ mentions |
miRSeqNovel (RRID:SCR_013257) | miRSeqNovel | software resource | An R/Bioconductor based workflow for novel miRNA prediction from deep sequencing data. |
is listed by: OMICtools has parent organization: SourceForge |
Free, Public, Non-commercial | OMICS_00381 | SCR_013257 | 2026-07-25 12:07:48 | 2 | |||||||||
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AutoMap Resource Report Resource Website 50+ mentions |
AutoMap (RRID:SCR_013095) | AutoMap | software resource | A tool for structural biology and drug design. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_01596 | SCR_013095 | 2026-07-25 12:07:44 | 92 | ||||||||||
|
DynamicProg Resource Report Resource Website |
DynamicProg (RRID:SCR_013217) | DynamicProg | software resource | A model-based statistical methods for base calling in Illumina''s next-generation sequencing platforms. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_01150 | SCR_013217 | 2026-07-25 12:07:47 | 0 | ||||||||||
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A Catalogue of Illusions Resource Report Resource Website |
A Catalogue of Illusions (RRID:SCR_013186) | image collection, data or information resource | Set of different illusions, including color illusions, motion illusions, and optic illusions. Most illusions are from Professor Akiyoshi Kitaoka of the Ritsumeikan University in Kyoto, Japan. | color, illusion, motion, optical, vision | has parent organization: Ritsumeikan University; Kyoto; Japan | nif-0000-24679 | SCR_013186 | Catalogue of Illusions | 2026-07-25 12:07:49 | 0 | |||||||||
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muliAlignFree Resource Report Resource Website |
muliAlignFree (RRID:SCR_013188) | muliAlignFree | software resource | R package intended to implement a program for multiple alignment-free sequence comparison based on long genome sequence or NGS data. |
is listed by: OMICtools has parent organization: University of Southern California; Los Angeles; USA |
PMID:23990418 | Free | OMICS_00981 | SCR_013188 | muliAlignFree: Multiple Alignment-free Sequence Comparison | 2026-07-25 12:07:47 | 0 | |||||||
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U.S. Public Health Service Commissioned Corps Resource Report Resource Website 1+ mentions |
U.S. Public Health Service Commissioned Corps (RRID:SCR_013104) | USPHS | institution | Commissioned Corps of the United States Public Health Service, is the federal uniformed service of the U.S. Public Health Service, and is one of the eight uniformed services of the United States. | Government granting agency | nlx_152565, Crossref funder ID: 100007197, ISNI: 0000 0001 1554 5300, grid.417684.8, Wikidata: Q476322 | https://ror.org/05xf94514 | SCR_013104 | US Public Health Service Commissioned Corps, U.S. Public Health Service | 2026-07-25 12:07:45 | 7 | ||||||||
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National Institute for Occupational Safety and Health Resource Report Resource Website |
National Institute for Occupational Safety and Health (RRID:SCR_013180) | NIOSH, OH | institution | http://www.cdc.gov/niosh/oep/funding.html |
has parent organization: Centers for Disease Control and Prevention is parent organization of: Adult Blood Lead Epidemiology and Surveillance Interactive Database |
nlx_inv_1005099, grid.416809.2, ISNI: 0000 0004 0423 0663, Wikidata: Q60346, Crossref funder ID: 100000125 | https://ror.org/0502a2655 | SCR_013180 | 2026-07-25 12:07:46 | 0 | |||||||||
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CancerMutationAnalysis Resource Report Resource Website |
CancerMutationAnalysis (RRID:SCR_013181) | CancerMutationAnalysis | software resource | Software package that implements gene and gene-set level analysis methods for somatic mutation studies of cancer. |
is listed by: OMICtools has parent organization: Bioconductor |
Cancer | OMICS_00141 | SCR_013181 | 2026-07-25 12:07:49 | 0 | |||||||||
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BEADS Resource Report Resource Website 10+ mentions |
BEADS (RRID:SCR_013229) | BEADS | software resource | Software for a normalization scheme that corrects nucleotide composition bias, mappability variations and differential local DNA structural effects in deep sequencing data. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge has parent organization: University of Cambridge; Cambridge; United Kingdom |
PMID:21646344 | OMICS_00466, biotools:beads | https://bio.tools/beads | SCR_013229 | BEADS: Bias Elimination Algorithm for Deep Sequencing, Bias Elimination Algorithm for Deep Sequencing | 2026-07-25 12:07:46 | 37 | ||||||
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LifeScope Resource Report Resource Website 100+ mentions |
LifeScope (RRID:SCR_013234) | LifeScope | software resource | Genomic Analysis Software designed to match the accuracy of the next generation 5500 Genetic Analyzers with Exact Call Chemistry (ECC). | unix/linux, life technologies, linux, next-generation sequencing | has parent organization: Life Technologies | Acknowledgement requested | OMICS_00667 | SCR_013234 | LifeScope Genomic Analysis Software | 2026-07-25 12:07:50 | 199 | |||||||
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CongrPE Resource Report Resource Website 1+ mentions |
CongrPE (RRID:SCR_013190) | CongrPE | software resource | A de novo assembly algorithm for Next-Generation Sequencing technology. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00011 | SCR_013190 | 2026-07-25 12:07:45 | 1 |
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