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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
VDJFasta Resource Report Resource Website 1+ mentions |
VDJFasta (RRID:SCR_013069) | VDJFasta | software resource | Bioinformatics Perl extension for the analysis of antibody variable domain repertoires. |
is listed by: OMICtools has parent organization: SourceForge |
PMID:19875695 | OMICS_00004 | SCR_013069 | 2026-02-07 02:08:42 | 8 | |||||||||
|
VCAKE Resource Report Resource Website 1+ mentions |
VCAKE (RRID:SCR_013060) | VCAKE | software resource | A genetic sequence assembler capable of assembling millions of small nucleotide reads even in the presence of sequencing error. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00037 | SCR_013060 | 2026-02-07 02:08:41 | 4 | ||||||||||
|
SpliceGrapher Resource Report Resource Website 10+ mentions |
SpliceGrapher (RRID:SCR_006657) | SpliceGrapher | software resource | Software that predicts alternative splicing patterns and produces splice graphs that capture in a single structure the ways a gene''s exons may be assembled. It enhances gene models using evidence from next-generation sequencing and EST alignments. |
is listed by: OMICtools has parent organization: SourceForge |
PMID:22293517 | OMICS_01266 | SCR_006657 | 2026-02-07 02:07:32 | 22 | |||||||||
|
MAGMA Resource Report Resource Website 100+ mentions |
MAGMA (RRID:SCR_005757) | MAGMA | software resource | Software that utilizes a multiobjective evolutionary algorithm for genetic mapping. It is based on a the ECJ evolutionary software package written by Sean Luke and includes the Strength Pareto Evoluationary Algorithm Version 2 changes for multiobjective analysis. The code runs on any platform with Java Version 2. A genetic mapping project, typically implemented during a search for genes responsible for a disease, requires the acquisition of a set of data from each of a large number of individuals. This data set includes the values of multiple genetic markers. These genetic markers occur at discrete positions along the genome, which is a collection of one or more linear chromosomes. Typing the value of a marker in an individual carries a cost; one seeks to minimize the number of markers typed without excessively jeopardizing the probability of detecting an association between a marker and a disease phenotype. MAGMA is a project which employ''s a multiobjective evolutionary algorithm to solve this problem. | gene, genetic mapping, algorithm, genomics, single nucleotide polymorphism, population study, haplotype-block elucidation, java | has parent organization: SourceForge | Juvenile Diabetes Research Foundation | PMID:12875658 | Open unspecified license | nlx_149220 | SCR_005757 | Multiobjective Analyzer for Genetic Marker Acquisition, MAGMA: Multiobjective Analyzer for Genetic Marker Acquisition | 2026-02-07 02:06:50 | 415 | |||||
|
Taipan Resource Report Resource Website 1+ mentions |
Taipan (RRID:SCR_007330) | Taipan | software resource | A fast hybrid short-read assembly tool. | c, unix/linux, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:19535537 | GNU General Public License, v2 | OMICS_00035, biotools:taipan | https://bio.tools/taipan | SCR_007330 | 2026-02-07 02:07:39 | 2 | ||||||
|
POLGUI - Matlab Polhemus Interface Resource Report Resource Website 1+ mentions |
POLGUI - Matlab Polhemus Interface (RRID:SCR_006752) | POLGUI | software resource | An interface between MATLAB and the Polhemus Fastrak digitizer used to digitize fiducial locations and scalp EEG electrode locations. There are 5 versions all of which work under MATLAB R14 (on both linux and windows platforms), # polgui_ver1_r14 : works with 1 receiver (stylus pen) # polgui_ver2_r14 : works with 2 receivers (including the pen) # polgui_ver3_r14 : works with 3 receivers(including the pen) # polgui_ver4_r14 : works with 4 receivers (including the pen) # polgui_ver5_r14 : Generic version which works with 1/2/3/4 receivers (WARNING: Ver 5 might be buggy; not fully tested) Requirements: MATLAB R14 (Linux/Windows) | eeg, meg, electrocorticography, linux, matlab, microsoft, magnetic resonance, posix/unix-like, win32 (ms windows), windows |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: SourceForge |
BSD License | nlx_155915 | http://www.nitrc.org/projects/polgui | SCR_006752 | POLGUI - Matlab GUI for Polhemus Fastrak | 2026-02-07 02:07:15 | 3 | ||||||
|
mubiomics Resource Report Resource Website 1+ mentions |
mubiomics (RRID:SCR_006785) | mubiomics | software resource | A set of scripts (mostly python) for processing reads generated by the Roche 454 or Illumina next-gen sequencing platforms. Included are quality control, read demultiplexing and microbiome characterisation scripts for use with usearch, pplacer and RDP classifier. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_01059 | SCR_006785 | mubiomics - Scripts for processing next-gen sequencing data | 2026-02-07 02:07:26 | 3 | |||||||||
|
Qudaich Resource Report Resource Website |
Qudaich (RRID:SCR_006775) | Qudaich | software resource | A software package for local sequence alignment for next-generation sequencing (NGS) data. It generates the pairwise local alignments between a query dataset against a database. The main design purpose of qudaich is to focus on datasets from next generation sequencing. These the datasets generally have hundreds of thousand sequences or more, and so, the input database should contain large number of sequences. Qudaich is flexible and its algorithmic structure imposes no restriction on the absolute limit of the acceptable read length, but the current version of qudaich allow read length <2000 bp. Qudaich can be used to align DNA, translated DNA and protein sequences. | next-generation sequencing, alignment |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00678 | SCR_006775 | Queries and unique database alignment inferred by clustering homologs | 2026-02-07 02:07:25 | 0 | ||||||||
|
GBS barcode splitter Resource Report Resource Website |
GBS barcode splitter (RRID:SCR_006799) | GBS barcode splitter | software resource | PERL script used to split barcode of Illumina sequencing data created by GBS protocol (www.maizegenetics.net). The barcode has variable size. Paired-end reads are supported. | illumina |
is listed by: OMICtools has parent organization: SourceForge |
Free | OMICS_01050 | SCR_006799 | GBS barcode splitter - PERL script for split GBS reads by barcode | 2026-02-07 02:07:34 | 0 | |||||||
|
BAMStats Resource Report Resource Website 10+ mentions |
BAMStats (RRID:SCR_006973) | BAMStats | software resource | A GUI desktop tool for calculating and displaying metrics to assess the success of Next Generation Sequencing mapping tools. BAMstats is written in Java and based around the Picard API. | matlab, next generation sequencing, java |
is listed by: OMICtools has parent organization: SourceForge |
GNU General Public License | OMICS_01034 | SCR_006973 | 2026-02-07 02:07:36 | 10 | ||||||||
|
BarraCUDA Resource Report Resource Website 1+ mentions |
BarraCUDA (RRID:SCR_006881) | BarraCUDA | software resource | A sequence mapping software that utilizes the massive parallelism of graphics processing units to accelerate the inexact alignment of short sequence reads to a particular location on a reference genome. It can align a paired-end library containing 14 million pairs of 76bp reads to the Human genome in about 27 minutes (from fastq files to SAM alignment) using a ��380 NVIDIA Geforce GTX 680*. The alignment throughput can be boosted further by using multiple GPUs (up to 8) at the same time. Being based on BWA (http://bio-bwa.sf.net) from the Sanger Institute, BarraCUDA delivers a high level of alignment fidelity and is comparable to other mainstream alignment programs. It can perform gapped alignment with gap extensions, in order to minimise the number of false variant calls in re-sequencing studies. | gpu/cuda, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Cambridge; Cambridge; United Kingdom has parent organization: SourceForge |
PMID:22244497 PMID:19451168 |
Acknowledgement requested | OMICS_00650, biotools:barracuda | https://bio.tools/barracuda | SCR_006881 | 2026-02-07 02:07:16 | 4 | ||||||
|
Gecko Resource Report Resource Website 100+ mentions |
Gecko (RRID:SCR_009001) | Gecko | software resource | A complete, high-capacity centralized gene expression analysis system, developed in response to the needs of a distributed user community. |
is listed by: OMICtools has parent organization: SourceForge |
PMID:15588317 | OMICS_00758 | SCR_009001 | Gene Expression: Computation and Knowledge Organization, Geckoe | 2026-02-07 02:07:51 | 493 | ||||||||
|
SCALCE Resource Report Resource Website |
SCALCE (RRID:SCR_009658) | SCALCE | software resource | A FASTQ compression tool that uses locally consistent parsing to obtain better compression rate. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00969 | SCR_009658 | Boosting Sequence Compression Algorithms using Locally Consistent Encoding | 2026-02-07 02:07:55 | 0 | |||||||||
|
vipR Resource Report Resource Website 50+ mentions |
vipR (RRID:SCR_010685) | vipR | software resource | A software program to screen for sequence variants (SNPs, deletions) in sequence data generated by high-throughput-sequencing platforms. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00081 | SCR_010685 | 2026-02-07 02:07:50 | 58 | ||||||||||
|
CoNIFER Resource Report Resource Website 100+ mentions |
CoNIFER (RRID:SCR_013213) | CoNIFER | software resource | Uses exome sequencing data to find copy number variants (CNVs) and genotype the copy-number of duplicated genes. |
is listed by: OMICtools has parent organization: SourceForge |
Commercial license | OMICS_00330 | SCR_013213 | Copy Number Inference From Exome Reads | 2026-02-07 02:08:46 | 191 | ||||||||
|
RDXplorer Resource Report Resource Website 1+ mentions |
RDXplorer (RRID:SCR_013290) | RDXplorer | software resource | A computational tool for copy number variants (CNV) detection in whole human genome sequence data using read depth (RD) coverage. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
biotools:RDXplorer, OMICS_00349 | https://bio.tools/RDXplorer | SCR_013290 | 2026-02-07 02:08:48 | 7 | ||||||||
|
PIA Resource Report Resource Website |
PIA (RRID:SCR_013267) | PIA | software resource | A prefix indexing and alignment software for next-generation sequencing (NGS) for whole human genome. | next-generation sequencing |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00676 | SCR_013267 | 2026-02-07 02:09:00 | 0 | |||||||||
|
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 | 2026-02-07 02:09:00 | 2 | |||||||||
|
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 | 2026-02-07 02:08:56 | 87 | ||||||||||
|
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 | 2026-02-07 02:08:46 | 0 |
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