Searching the RRID Resource Information Network
Are you sure you want to leave this community? Leaving the community will revoke any permissions you have been granted in this community.
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.
| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
ChimeraSlayer Resource Report Resource Website 100+ mentions |
ChimeraSlayer (RRID:SCR_013283) | ChimeraSlayer | software resource | A chimeric sequence detection utility, compatible with near-full length Sanger sequences and shorter 454-FLX sequences (~500 bp). | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
OMICS_01113, biotools:chimeraslayer | https://bio.tools/chimeraslayer | SCR_013283 | SciCrunch Registry | 2026-10-31 12:15:55 | 320 | ||||||||
|
Telescoper Resource Report Resource Website |
Telescoper (RRID:SCR_013206) | Telescoper | software resource | An algorithm that iteratively extends long paths through a series of read-overlap graphs and evaluates them based on a statistical framework. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:22962446 | biotools:telescoper, OMICS_00036 | https://bio.tools/telescoper | SCR_013206 | SciCrunch Registry | Telescoper - De novo assembly algorithm | 2026-10-31 12:15:52 | 0 | ||||||
|
dbCAN Resource Report Resource Website 500+ mentions |
dbCAN (RRID:SCR_013208) | dbCAN | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | A web server and DataBase for automated Carbohydrate-active enzyme ANnotation, funded by the BioEnergy Science Center of the DOE., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | FASEB list | is listed by: OMICtools | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01678 | SCR_013208 | SciCrunch Registry | 2026-10-31 12:15:56 | 725 | ||||||||
|
palfinder Resource Report Resource Website 1+ mentions |
palfinder (RRID:SCR_013174) | palfinder | software resource | A perl script that finds microsatellite repeat elements directly from raw 454 or Illumina paired-end sequencing reads. | pacific biosciences |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00111 | SCR_013174 | SciCrunch Registry | 2026-10-31 12:15:53 | 6 | |||||||||
|
IsoLasso Resource Report Resource Website 1+ mentions |
IsoLasso (RRID:SCR_013176) | IsoLasso | 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 |
OMICS_01320, biotools:isolasso | https://bio.tools/isolasso | SCR_013176 | SciCrunch Registry | 2026-10-31 12:15:55 | 3 | ||||||||
|
sam comp Resource Report Resource Website |
sam comp (RRID:SCR_013179) | sam_comp | software resource | A simple arithmetic coding based compressor for the SAM and BAM (DNA sequence alignment) file format. | c++ |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23533605 | OMICS_00968 | SCR_013179 | SciCrunch Registry | 2026-10-31 12:15:53 | 0 | ||||||||
|
HeurAA Resource Report Resource Website |
HeurAA (RRID:SCR_013212) | HeurAA | software resource | Software for accurate and fast detection of genetic variations with a novel heuristic amplicon aligner program for next generation sequencing. | unix/linux, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:23349847 | OMICS_00097, biotools:heuraa | https://bio.tools/heuraa | SCR_013212 | SciCrunch Registry | heurAA - NGS multiplexed amplicon aligner | 2026-10-31 12:15:52 | 0 | ||||||
|
bisReadMapper Resource Report Resource Website |
bisReadMapper (RRID:SCR_013171) | bisReadMapper | software resource | Fast and lightweight package for mapping bisulfite converted DNA sequencing reads from the Illumina platform. | illumina |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00576 | SCR_013171 | SciCrunch Registry | bisReadMapper - Software for dealing with DNA methylation sequencing data | 2026-10-31 12:15:55 | 0 | ||||||||
|
MACS Resource Report Resource Website 1000+ mentions |
MACS (RRID:SCR_013291) | MACS | data analysis software, data processing software, software application, software resource | Software Python package for identifying transcript factor binding sites. Used to evaluate significance of enriched ChIP regions. Improves spatial resolution of binding sites through combining information of both sequencing tag position and orientation. Can be used for ChIP-Seq data alone, or with control sample with increase of specificity. | identify, transcript, factor, binding, site, model, based, analysis, CHIP Seq, short, read, sequencer, protein, DNA, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: Dana-Farber Cancer Institute |
NHGRI HG004069; NHGRI HG004270; NIDDK DK074967 |
PMID:18798982 DOI:10.1186/gb-2008-9-9-r137 |
Free, Available for download, Freely available | OMICS_00446, biotools:macs | https://bio.tools/macs, https://sources.debian.org/src/macs/ | SCR_013291 | SciCrunch Registry | MACS - Model-based Analysis for ChIP-Seq, Model-based Analysis for ChIP-Seq, MACS2 | 2026-10-31 12:15:55 | 1418 | ||||
|
SeqTRACS Resource Report Resource Website |
SeqTRACS (RRID:SCR_013294) | SeqTRACS | software resource | Software for a Laboratory Information Management System (LIMS) for tracking, organizing, and accessing sequencing requests and ABI trace files produced by a centralized sequencing core facility. | matlab |
is listed by: OMICtools has parent organization: SourceForge |
GNU General Public License, v3 | OMICS_01013 | SCR_013294 | SciCrunch Registry | SeqTRACS: LIMS for sequencing core facilities | 2026-10-31 12:16:03 | 0 | |||||||
|
CEDER Resource Report Resource Website 10+ mentions |
CEDER (RRID:SCR_013255) | CEDER | software resource | R package intended to implement a program for detecting differentially expressed genes (DEG) using RNA-Seq by combining significance of exons within a gene. |
is listed by: OMICtools has parent organization: University of Southern California; Los Angeles; USA |
OMICS_01301 | SCR_013255 | SciCrunch Registry | 2026-10-31 12:15:53 | 11 | ||||||||||
|
GPSeq Resource Report Resource Website 1+ mentions |
GPSeq (RRID:SCR_013250) | GPSeq | software resource | A software tool to analyze RNA-seq data to estimate gene and exon expression, identify differentially expressed genes, and differentially spliced exons., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. |
is listed by: OMICtools has parent organization: University of Southern California; Los Angeles; USA |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01333 | SCR_013250 | SciCrunch Registry | 2026-10-31 12:16:02 | 6 | |||||||||
|
MAP Resource Report Resource Website 1+ mentions |
MAP (RRID:SCR_013216) | software resource | This resource is out of service. Documented on February 23,2021. Software for de novo metagenomic assembly program for shotgun DNA reads., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Peking University; Beijing; China |
PMID:22495746 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01424, biotools:MAP | https://bio.tools/MAP | SCR_013216 | SciCrunch Registry | Metagenomic Assembly Program | 2026-10-31 12:15:54 | 1 | ||||||
|
DiffSplice Resource Report Resource Website 10+ mentions |
DiffSplice (RRID:SCR_013215) | DiffSplice | software resource | The Genome-Wide Detection of Differential Splicing Events with RNA-seq. |
is listed by: OMICtools has parent organization: University of Kentucky; Kentucky; USA |
PMID:23155066 | OMICS_01330 | SCR_013215 | SciCrunch Registry | 2026-10-31 12:16:01 | 15 | |||||||||
|
genCAT Resource Report Resource Website 1+ mentions |
genCAT (RRID:SCR_013220) | genCAT | software resource | Software designed as an open platform that allows users to incorporate as many datasets (concepts) as possible to annotate the input gene list, as long as these datasets are prepared in bigwig, BED, BAM/SAM formats. |
is listed by: OMICtools has parent organization: Google Code |
GNU General Public License, v2 | OMICS_01416 | SCR_013220 | SciCrunch Registry | gencat - Gene''s Comprehensive Annotation Tool | 2026-10-31 12:16:01 | 6 | ||||||||
|
SOCS Resource Report Resource Website 50+ mentions |
SOCS (RRID:SCR_013223) | SOCS | software resource | Performs ungapped alignment of SOLiD (color space) sequencing reads against reference sequences. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00590 | SCR_013223 | SciCrunch Registry | 2026-10-31 12:15:54 | 91 | ||||||||||
|
PolyPhen: Polymorphism Phenotyping Resource Report Resource Website 1000+ mentions |
PolyPhen: Polymorphism Phenotyping (RRID:SCR_013189) | PolyPhen, PolyPhen-2, POLYPHEN | data analysis software, data processing software, simulation software, software application, software resource | Software tool which predicts possible impact of amino acid substitution on structure and function of human protein using straightforward physical and comparative considerations. PolyPhen-2 is new development of PolyPhen tool for annotating coding nonsynonymous SNPs. | annotate, nonsynonymous, SNP, predict, coding, damaging, effect, missense, mutation, sequence, variant, phenotype, genetic, disease, exon, protein, coding, fraction, genome, bio.tools |
is listed by: Genetic Analysis Software is listed by: Debian is listed by: bio.tools is related to: OMICtools has parent organization: Harvard University; Cambridge; United States |
PMID:20354512 PMID:23315928 |
SCR_013200, OMICS_00136, nlx_154540, nif-0000-21329, biotools:polyphen, SCR_013238 | https://bio.tools/polyphen | http://www.bork.embl-heidelberg.de/PolyPhen/ | SCR_013189 | SciCrunch Registry | PolyPhen, POLYPHEN, PolyPhen-2, Polymorphism Phenotyping, Polymorphism Phenotyping v2 | 2026-10-31 12:15:53 | 4723 | |||||
|
aCGH Resource Report Resource Website 100+ mentions |
aCGH (RRID:SCR_013232) | aCGH | software resource | Software functions for reading aCGH data from image analysis output files and clone information files, creation of aCGH S3 objects for storing these data. Basic methods for accessing/replacing, subsetting, printing and plotting aCGH objects. |
is listed by: OMICtools has parent organization: Bioconductor |
OMICS_00698 | SCR_013232 | SciCrunch Registry | 2026-10-31 12:16:01 | 136 | ||||||||||
|
DSP Resource Report Resource Website |
DSP (RRID:SCR_013114) | DSP | software resource | Pipeline for small genome assembly using SOLiD sequencing technology. |
is listed by: OMICtools has parent organization: SourceForge |
Apache License, v2 | OMICS_00013 | SCR_013114 | SciCrunch Registry | denovo_solid_pipeline | 2026-10-31 12:15:59 | 0 | ||||||||
|
RepeatSeq Resource Report Resource Website 10+ mentions |
RepeatSeq (RRID:SCR_013235) | RepeatSeq | software resource | Software that determines genotypes for microsatellite repeats in high-throughput sequencing data. | is listed by: OMICtools | PMID:23090981 | OMICS_00112 | SCR_013235 | SciCrunch Registry | 2026-10-31 12:15:53 | 18 |
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 dkNET Resources search. From here you can search through a compilation of resources used by dkNET and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that dkNET 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 dkNET then you can log in from here to get additional features in dkNET 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:
If you are logged into dkNET you can add data records to your collections to create custom spreadsheets across multiple sources of data.
Here are the facets that you can filter the data by.
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.
The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
Email: info_at_ dknet.org
