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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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NIDB - Neuroinformatics Database Resource Report Resource Website 1+ mentions |
NIDB - Neuroinformatics Database (RRID:SCR_002488) | NIDB | data management software, data or information resource, database, software application, software resource | Neuroimaging database designed to allow simple importing, searching, and sharing of imaging data. NIDB also provides automated pipelining with importing of results back into NIDB which can be searched along with imaging meta data. | connectome file format, clinical neuroinformatics, computational neuroscience, computed tomography, imaging genomics, interfile, javascript, neuroimaging |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: SourceForge |
PMID:25888923 | Free, Available for download, Freely available | nlx_155882 | http://www.nitrc.org/projects/nidb | http://nidb.sourceforge.net/ | SCR_002488 | SciCrunch Registry | Neuroinformatics Database | 2026-10-17 01:25:12 | 2 | ||||
|
SCRalyze Resource Report Resource Website 10+ mentions |
SCRalyze (RRID:SCR_002542) | SCRalyze | data analysis software, data processing software, software application, software resource | A powerful software for model-based analysis of peripheral psychophysiology (e.g. skin conductance, heart rate, pupil size etc.). General linear modelling and dynamic causal modelling of these signals provide for inference on neural states/processes. SCRalyze includes flexible data import and display, statistical inference and results display and export. Easy programming of add-ons for new data formats, signal channels, and models. | eeg, meg, electrocorticography, matlab, modeling, os independent, quantification, time domain analysis |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: SourceForge |
Free, Available for download, Freely available | nlx_155950 | http://www.nitrc.org/projects/scralyze | SCR_002542 | SciCrunch Registry | SCRalyze - A matlab environment for model-based psychophysiology | 2026-10-17 01:25:28 | 17 | ||||||
|
ANDES Resource Report Resource Website 10+ mentions |
ANDES (RRID:SCR_002791) | data analysis software, data processing software, software application, software resource, software toolkit | Software library and a suite of applications, written in Perl and R, for deep sequencing statistical analyses. | deep sequencing, biomarker detection, statistical analysis, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:20633290 | Free, Freely available, Available for download | biotools:andes, OMICS_01119 | https://bio.tools/andes | SCR_002791 | SciCrunch Registry | Statistical tools for the Analyses of Deep Sequencing (ANDES), Statistical tools for the Analyses of Deep Sequencing, Statistical tools for the ANalyses of Deep Sequencing | 2026-10-17 01:25:18 | 26 | ||||||
|
GLProbs Resource Report Resource Website 1+ mentions |
GLProbs (RRID:SCR_002739) | software resource | Software implementing a simple and effective approach to improve the accuracy of multiple sequence alignment. | standalone software |
is listed by: OMICtools has parent organization: SourceForge |
PMID:26357079 | Free, Freely available, Available for download | OMICS_03732 | SCR_002739 | SciCrunch Registry | 2026-10-17 01:25:17 | 1 | ||||||||
|
Rainbow Resource Report Resource Website 10+ mentions |
Rainbow (RRID:SCR_002724) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software developed to provide an ultra-fast and memory-efficient solution to clustering and assembling short reads produced by RAD-seq. | software, tool, clustering, assembling, short, read, restriction, site, DNA, sequence, analysis, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:22942077 DOI:10.1093/bioinformatics/bts482 |
Free, Freely available, Available for download | SCR_015992, OMICS_03722, biotools:rainbow | https://bio.tools/rainbow, https://sources.debian.org/src/bio-rainbow/ | SCR_002724 | SciCrunch Registry | RAD-seq: Restriction-site Associated DNA sequencing, Bio-rainbow, RAD-seq | 2026-10-17 01:25:16 | 41 | ||||||
|
rDock Resource Report Resource Website 100+ mentions |
rDock (RRID:SCR_002838) | software resource | A fast and versatile Open Source docking software program that can be used to dock small molecules against proteins and nucleic acids. | standalone software |
is listed by: OMICtools has parent organization: SourceForge |
PMID:24722481 | Free, Freely available, Available for download | OMICS_03835 | SCR_002838 | SciCrunch Registry | 2026-10-17 01:25:36 | 122 | ||||||||
|
FAS-DPD Resource Report Resource Website |
FAS-DPD (RRID:SCR_003068) | FAS-DPD | software resource | Software program to design degenerate primers for PCR. | command-line, java, primer, pcr, degenerate primer |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23533783 | Free, Available for download, Freely available | OMICS_02340 | SCR_003068 | SciCrunch Registry | family-specific degenerate primer design | 2026-10-17 01:25:23 | 0 | ||||||
|
riboPicker Resource Report Resource Website 1+ mentions |
riboPicker (RRID:SCR_000360) | software resource | Software to automatically identify and efficiently remove rRNA-like sequences from metatranscriptomic and metagenomic datasets. | standalone software, perl, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:22155869 | Free, Available for download, Freely available | OMICS_02618, biotools:ribopicker | https://bio.tools/ribopicker | SCR_000360 | SciCrunch Registry | 2026-10-17 01:24:41 | 2 | |||||||
|
ParseCNV Resource Report Resource Website 1+ mentions |
ParseCNV (RRID:SCR_000355) | software resource | Software that takes CNV calls as input and creates SNP based statistics for CNV occurrence in cases and controls then calls CNVRs based on neighboring SNPs of similar significance. | standalone software |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23293001 | Free, Available for download, Freely available | OMICS_02566 | SCR_000355 | SciCrunch Registry | 2026-10-17 01:24:37 | 1 | ||||||||
|
Kinannote Resource Report Resource Website 1+ mentions |
Kinannote (RRID:SCR_000352) | software resource | Software that identifies and classifies protein kinases in a user-provided fasta file using an HMM derived from serine / threonine protein kinases, a position specific scoring matrix derived from the HMM, and comparison with a local version of the curated kinase database from kinase.com. | standalone software, perl |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23904509 | Free, Available for download, Freely available | OMICS_05965 | SCR_000352 | SciCrunch Registry | 2026-10-17 01:24:38 | 2 | ||||||||
|
Jnomics Resource Report Resource Website |
Jnomics (RRID:SCR_000348) | software resource | A collection of cloud-scale DNA sequence analysis tools. | mapreduce |
is listed by: OMICtools has parent organization: SourceForge |
Free, Available for download, Freely available | OMICS_04074 | SCR_000348 | SciCrunch Registry | 2026-10-17 01:24:38 | 0 | |||||||||
|
fqzcomp Resource Report Resource Website 1+ mentions |
fqzcomp (RRID:SCR_000299) | fqzcomp | software resource | A basic fastq compressor, designed primarily for high performance. | c++ |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23533605 | Free, Available for download, Freely available | OMICS_00957 | SCR_000299 | SciCrunch Registry | 2026-10-17 01:24:39 | 1 | |||||||
|
miRprimer Resource Report Resource Website 1+ mentions |
miRprimer (RRID:SCR_000480) | miRprimer | software resource | Software tool for automatic design of primers for PCR amplification of microRNAs using the method miR-specific RT-qPCR (Balcells, I., Cirera, S., and Busk, P.K. (2011). Specific and sensitive quantitative RT-PCR of miRNAs with DNA primers. BMC Biotechnol. 11, 70). | ruby, primer, microrna, rt-qpcr, ms windows, pcr amplification |
is listed by: OMICtools has parent organization: SourceForge |
PMID:24472427 | Free, Available for download, Freely available | OMICS_02311 | SCR_000480 | SciCrunch Registry | miRprimer - Automatic design of primers for miR-specific RT-qPCR | 2026-10-17 01:24:40 | 3 | ||||||
|
BAIT Resource Report Resource Website 1+ mentions |
BAIT (RRID:SCR_000511) | BAIT | data analysis software, data processing software, data visualization software, software application, software resource | Software to create strand inheritance plots in data derived from the Strand-Seq sequencing protocol. The software is designed to be flexible with a range of species, and basic template folders can called to read in species-specific data. | create strand inheritance plots, strand-seq, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:24028793 | Free, Available for download, Freely available | biotools:bait, OMICS_01531 | https://bio.tools/bait | SCR_000511 | SciCrunch Registry | BAIT - Software to help analyse Strand-Seq data | 2026-10-17 01:24:42 | 1 | |||||
|
pyQPCR Resource Report Resource Website |
pyQPCR (RRID:SCR_000471) | pyQPCR | software resource | A GUI application written in python that deals with quantitative PCR (QPCR) raw data. Using quantification cycle values extracted from QPCR instruments, it uses a proven and universally applicable model to give finalized quantification resu | quantitative pcr, python, qt |
is listed by: OMICtools has parent organization: SourceForge |
Free, Available for download, Freely available | OMICS_02326 | SCR_000471 | SciCrunch Registry | 2026-10-17 01:24:40 | 0 | ||||||||
|
POPBAM Resource Report Resource Website |
POPBAM (RRID:SCR_000464) | POPBAM | data analysis software, data processing software, software application, software resource | A tool to perform evolutionary or population-based analyses of next-generation sequencing data. POPBAM takes a BAM file as its input and can compute many widely used evolutionary genetics measures in sliding windows across a genome. | next-generation sequencing, evolution, population, bam, genome, evolutionary genetics, c++, short read, sequence alignment, sliding window, command-line, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge has parent organization: University of Rochester; New York; USA |
PMID:24027417 | Free, Available for download, Freely available | biotools:popbam, OMICS_01559 | https://bio.tools/popbam | http://popbam.sourceforge.net/ | SCR_000464 | SciCrunch Registry | 2026-10-17 01:24:44 | 0 | |||||
|
drFAST Resource Report Resource Website 1+ mentions |
drFAST (RRID:SCR_000586) | drFAST | software resource | A software which maps di-base reads (SOLiD color space reads) to reference genome assemblies in a fast and memory-efficient manner. | di-base, solid color space, genome assemblies, memory-efficient, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: SPLITREAD has parent organization: SourceForge |
PMID:21586516 | Free, Available for download, Freely available | biotools:drfast, OMICS_00661 | https://bio.tools/drfast | SCR_000586 | SciCrunch Registry | di-base read Fast Alignment Search Tool, drFAST: di-base read Fast Alignment Search Tool | 2026-10-17 01:24:43 | 1 | |||||
|
GMcloser Resource Report Resource Website 1+ mentions |
GMcloser (RRID:SCR_000646) | GMcloser | software resource | Software that fills and closes the gaps present in scaffold assemblies, especially those generated by the de novo assembly of whole genomes with next-generation sequencing (NGS) reads. Unlike other gap-closing tools that use only NGS reads, GMcloser uses preassembled contig sets or long read sets as the sequences to close gaps and uses paired-end (PE) reads and a likelihood-based algorithm to improve the accuracy and efficiency of gap closure. The efficiency of gap closure can be increased by successive treatments with different contig sets. | scaffolding, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:26261222 | Free, Available for download, Freely available | biotools:gmcloser, OMICS_00042 | https://bio.tools/gmcloser | SCR_000646 | SciCrunch Registry | Gmcloser - Closing the gaps in scaffolds with preassembled contigs | 2026-10-17 01:24:44 | 3 | |||||
|
detecttd Resource Report Resource Website |
detecttd (RRID:SCR_000681) | detecttd | software resource | Software tool to detect tandem duplications in sequencing reads. It is written in Python and requires NCBI Blast standalone. | tandem duplication, sequencing read, python, next-generation sequencing |
is listed by: OMICtools has parent organization: SourceForge |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00315 | SCR_000681 | SciCrunch Registry | detecttd - Tool to detect tandem duplications in NGS reads | 2026-10-17 01:24:43 | 0 | |||||||
|
FastUniq Resource Report Resource Website 1+ mentions |
FastUniq (RRID:SCR_000682) | software resource | A software tool for removal of de novo duplicates in paired short DNA sequences. | de novo, dna, sequence, duplicate, |
is listed by: OMICtools has parent organization: SourceForge |
DOI:10.1371/journal.pone.0052249 | Free, Available for download, Freely available | OMICS_01044 | SCR_000682 | SciCrunch Registry | 2026-10-17 01:24:45 | 4 |
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