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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
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 | 2026-02-14 02:02:28 | 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 | 2026-02-14 02:02:51 | 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 | 2026-02-14 02:02:21 | 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 | 2026-02-14 02:02:28 | 0 | ||||||||||
|
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 | 2026-02-14 02:02:50 | 37 | ||||||
|
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 | 2026-02-14 02:02:28 | 1 | ||||||||||
|
CallSim Resource Report Resource Website |
CallSim (RRID:SCR_013192) | CallSim | software resource | A software application that provides evidence for the validity of base calls believed to be sequencing errors and it is applicable to Ion Torrent and 454 data. | matlab |
is listed by: OMICtools has parent organization: SourceForge |
Apache License | OMICS_01098 | SCR_013192 | CallSim - Low-volume read processing base corrector | 2026-02-14 02:02:22 | 0 | |||||||
|
SAPAS Resource Report Resource Website 50+ mentions |
SAPAS (RRID:SCR_013195) | SAPAS | software resource | A RNA-seq method for polyA research. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_01413 | SCR_013195 | 2026-02-14 02:02:28 | 66 | ||||||||||
|
ArrayOligoSelector Resource Report Resource Website 10+ mentions |
ArrayOligoSelector (RRID:SCR_013494) | ArrayOligoSelector | software resource | Software program to systematically design gene specific long oligonucleotide probes for entire genomes, for the purpose of developing whole genome microarrays. For each open reading frame, the program optimizes the oligo selection based upon several parameters, including uniqueness in the genome, sequence complexity, lack of self-binding, GC content and proximity to the 3''end of the gene. |
is listed by: OMICtools has parent organization: University of California at San Francisco; California; USA has parent organization: SourceForge |
PMID:12620119 | Free, Public, Commercial requires license, Use of the blat or gfclient options requires license | OMICS_00826 | SCR_013494 | 2026-02-14 02:02:30 | 13 | ||||||||
|
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 | 2026-02-14 02:01:13 | 22 | |||||||||
|
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 | 2026-02-14 02:01:12 | 4 | ||||||
|
Ray Meta Resource Report Resource Website 10+ mentions |
Ray Meta (RRID:SCR_011918) | Ray Meta | software resource | Software for a massively distributed metagenome assembler that is coupled with Ray Communities, which profiles microbiomes based on uniquely-colored k-mers. | c++ |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23259615 | Free | OMICS_01431 | SCR_011918 | 2026-02-14 02:02:31 | 12 | |||||||
|
miRPlant Resource Report Resource Website 10+ mentions |
miRPlant (RRID:SCR_012105) | software resource | A user-friendly plant miRNA prediction tool. | applet, unix/linux, mac os x, windows, java, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:25117656 | GNU General Public License | OMICS_05325, biotools:mirplant | https://bio.tools/mirplant | SCR_012105 | 2026-02-14 02:02:36 | 14 | |||||||
|
PyPedal Resource Report Resource Website 1+ mentions |
PyPedal (RRID:SCR_012104) | software resource | A pedigree analysis software package that provides tools for error checking, mathematical analysis, report generation, pedigree simulation, and data visualization. | standalone software |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_05311 | SCR_012104 | 2026-02-14 02:02:18 | 2 | ||||||||||
|
Simulate PCR Resource Report Resource Website |
Simulate PCR (RRID:SCR_012106) | software resource | Software that can be run from the command line for high throughput applications which can calculate all products from large lists of primers and probes compared to a large sequence database such as nt. | standalone software, perl |
is listed by: OMICtools has parent organization: SourceForge |
PMID:25005023 | Free, Public | OMICS_05372 | SCR_012106 | 2026-02-14 02:02:10 | 0 | ||||||||
|
SAT-Assembler Resource Report Resource Website 1+ mentions |
SAT-Assembler (RRID:SCR_012108) | software resource | A targeted gene assembly software program which aims to recover gene families of particular interest to biologists. | standalone software, python |
is listed by: OMICtools has parent organization: SourceForge |
PMID:25122209 | Creative Commons License | OMICS_05397 | SCR_012108 | 2026-02-14 02:02:18 | 3 | ||||||||
|
FingerID Resource Report Resource Website 10+ mentions |
FingerID (RRID:SCR_012077) | software resource | A metabolite identification software using tandem mass spectrometry and kernel methods. | standalone software, matlab, python |
is listed by: OMICtools has parent organization: SourceForge |
PMID:22815355 | GNU General Public License | OMICS_04649 | SCR_012077 | 2026-02-14 02:02:34 | 18 | ||||||||
|
proTRAC Resource Report Resource Website 10+ mentions |
proTRAC (RRID:SCR_012078) | software resource | A software which detects and analyses piRNA clusters based on quantifiable deviations from a hypothetical uniform distribution regarding the decisive piRNA cluster characteristics. | standalone software, perl |
is listed by: OMICtools has parent organization: SourceForge |
PMID:22233380 | Creative Commons License | OMICS_04874 | SCR_012078 | probabilistic TRacking and Analysis of Clusters | 2026-02-14 02:02:18 | 26 | |||||||
|
NetMODE Resource Report Resource Website 1+ mentions |
NetMODE (RRID:SCR_012085) | software resource | Fast motif detection algorithm for subgraph size no more than 6. | standalone software |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23272055 | OMICS_05019 | SCR_012085 | 2026-02-14 02:02:34 | 1 | |||||||||
|
SketchEl Resource Report Resource Website |
SketchEl (RRID:SCR_012082) | software resource | An interactive chemical molecule sketching tool, and molecular spreadsheet data entry application. | applet, mac os x, unix/linux, windows, java, javascript |
is listed by: OMICtools has parent organization: SourceForge |
GNU General Public License | OMICS_04982 | SCR_012082 | 2026-02-14 02:02:18 | 0 |
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