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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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seqmagick Resource Report Resource Website 1+ mentions |
seqmagick (RRID:SCR_024331) | software resource, source code | Software application to expose file format conversion in BioPython in convenient way. Imagemagick like frontend to Biopython SeqIO. | file format conversion in BioPython, | is listed by: Debian | Free, Available for download, Freely available, | OMICS_11290 | https://sources.debian.org/src/seqmagick/ | SCR_024331 | 2026-08-12 10:53:12 | 2 | ||||||||
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LinearSVC Resource Report Resource Website 1+ mentions |
LinearSVC (RRID:SCR_024741) | software resource, software application | Software application for linear support vector classification. Used in classification problems. | linear support vector classification, classification problems, | Free, Freely available | SCR_024741 | Linear Support Vector Classification | 2026-08-12 10:53:12 | 3 | ||||||||||
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SingleCellNet Resource Report Resource Website 1+ mentions |
SingleCellNet (RRID:SCR_024742) | software resource, software application | Software tool to classify single cell RNA-Seq data across platforms and across species. | classify single cell RNA-Seq data, data across platforms and across species classification, | PMID:31377170 | Free, Available for download, Freely available | SCR_024742 | 2026-08-12 10:53:10 | 2 | ||||||||||
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Htscodecs Resource Report Resource Website |
Htscodecs (RRID:SCR_024034) | software resource, source code | Software repository implements the custom CRAM codecs used for "EXTERNAL" block types.Custom compression for CRAM custom algorithm written to compress the BAM file format for DNA sequencing data. | custom CRAM codecs, EXTERNAL" block types, custom compression for CRAM, compress the BAM file format, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/htscodecs/ | SCR_024034 | htscodecs | 2026-08-12 10:53:08 | 0 | ||||||||
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SlicerMorph Resource Report Resource Website 1+ mentions |
SlicerMorph (RRID:SCR_024674) | software resource, source code | Open and extensible platform to retrieve, visualize and analyse 3D morphology.Extension to import microCT data and conduct 3D morphometrics in Slicer. Used for data import, visualization, measurement, annotation, and geometric morphometric analysis on 3D data, including volumetric scans (CTs and MRs) and 3D surface scans, all within the 3D Slicer application. | retrieve, visualize, analyse 3D morphology, import microCT data extension, data import, visualization, measurement, annotation, geometric morphometric analysis, 3D data, volumetric scans, 3D surface scans | works with: 3D Slicer | NSF Advances in Biological Informatics | DOI:10.1111/2041-210X.13669 | Free, Available for download, Freely available | SCR_024674 | 2026-08-12 10:53:11 | 3 | ||||||||
|
rpy2 Resource Report Resource Website 10+ mentions |
rpy2 (RRID:SCR_024701) | software resource, source code | Software interface to use R from Python. | interface, R, Python | https://github.com/rpy2/rpy2 | SCR_024701 | 2026-08-12 10:53:17 | 11 | |||||||||||
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ELPH Resource Report Resource Website |
ELPH (RRID:SCR_024011) | software resource, source code | Software tool as general purpose Gibbs sampler for finding motifs in set of DNA or protein sequences.Takes as input a set containing sequences, and searches through them for the most common motif, assuming that each sequence contains one copy of the motif. Used to find patterns such as ribosome binding sites (RBSs) and exon splicing enhancers (ESEs). | Gibbs sampler, finding motifs, DNA sequences, protein sequences, common motif search, find patterns, ribosome binding sites, exon splicing enhancers, | is listed by: Debian | Free, Available for download, Freely available | OMICS_24617 | https://sources.debian.org/src/elph/ | SCR_024011 | Estimated Locations of Pattern Hits, elph | 2026-08-12 10:53:01 | 0 | |||||||
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ms-variability-analysis Resource Report Resource Website 1+ mentions |
ms-variability-analysis (RRID:SCR_024531) | software resource, source code | Variability analysis of proteomics data used for deep learning. | Variability analysis, proteomics data, | Free, Available for download, Freely available | SCR_024531 | 2026-08-12 10:53:06 | 1 | |||||||||||
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CCS Resource Report Resource Website 10+ mentions |
CCS (RRID:SCR_024379) | software resource, source code | Software to generate highly accurate single molecule consensus reads. | HiFi Reads, generate highly accurate single molecule consensus reads, generate consensus reads, | is listed by: Debian | Free, Available for download, Freely available, | OMICS_26281 | https://sources.debian.org/src/unanimity/ | SCR_024379 | ccs ; unanimity | 2026-08-12 10:53:13 | 32 | |||||||
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Fast5 Library Resource Report Resource Website |
Fast5 Library (RRID:SCR_024023) | software resource, source code | Software C++ library for accessing Oxford Nanopore Technologies sequencing data. | C++ library, accessing Oxford Nanopore Technologies sequencing data, | is listed by: Debian | Free, Available for download, Freely available | OMICS_29589 | https://sources.debian.org/src/fast5/ | SCR_024023 | Fast5, fast5 | 2026-08-12 10:52:56 | 0 | |||||||
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TADA-A Resource Report Resource Website |
TADA-A (RRID:SCR_024538) | software resource, source code | Software statistical framework for mapping risk genes from de novo mutations in whole genome sequencing studies. | mapping risk genes, de novo mutations, whole genome sequencing, | NIMH R01MH110531; Simons Foundation |
PMID:29754769 | Free, Available for download, Freely available | SCR_024538 | TADA-Annotations | 2026-08-12 10:53:06 | 0 | ||||||||
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python-biom-format Resource Report Resource Website 1+ mentions |
python-biom-format (RRID:SCR_024193) | software resource, source code | Software provides command line interface and Python API for working with Biological Observation Matrix files. | command line interface, Python API for working with Biological Observation Matrix files, BIOM files, |
is listed by: Debian is related to: biomformat |
PMID:23587224 | Free, Available for download, Freely available, | https://sources.debian.org/src/python3-biom-format/ | SCR_024193 | 2026-08-12 10:53:01 | 3 | ||||||||
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MetaPSICOV Resource Report Resource Website 1+ mentions |
MetaPSICOV (RRID:SCR_024517) | software resource, source code | Software tool for accurate prediction of contacts and long range hydrogen bonding in proteins. | accurate prediction, contacts and long range hydrogen bonding in proteins prediction, | is listed by: SoftCite | PMID:25431331 | Free, Available for download, Freely available | SCR_024517 | 2026-08-12 10:53:09 | 2 | |||||||||
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MCFLIRT Resource Report Resource Website 1+ mentions |
MCFLIRT (RRID:SCR_024792) | software resource, software application | Software intra-modal motion correction tool designed for use on fMRI time series for linear (affine) inter- and inter-modal brain image registration. | registration for brain images, medical image analysis, motion correction, | is a plug in for: FSL | Free, Freely available | SCR_024792 | Motion Correction FMRIB's Linear Image Registration Tool, , MC FMRIB's Linear Image Registration Tool | 2026-08-12 10:53:18 | 4 | |||||||||
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DeepDraw Resource Report Resource Website |
DeepDraw (RRID:SCR_024840) | software resource, source code | Software application for creating scalable muscle spindles dataset based on kinematic data and define action recognition task as benchmark. Training and analysis of hierarchical neural networks to solve recognition task from muscle spindle inputs. | Training and analysis of hierarchical neural networks, solve recognition task, muscle spindle inputs, | Free, Available for download, Freely available | SCR_024840 | 2026-08-12 10:53:14 | 0 | |||||||||||
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bulkGAN Resource Report Resource Website |
bulkGAN (RRID:SCR_024798) | software resource, software application | Software tool for scRNA and spatial transcriptomics.Used to generate RNA data close to real bulk RNA-seq with constraints of scRNA-seq data, based on keras and tensflow framework. | GANs, bulk RNA-seq, scRNA-seq, spatial transcriptomics, | Free, Available for download, Freely available | https://codeocean.com/capsule/8144402/tree | SCR_024798 | 2026-08-12 10:53:18 | 0 | ||||||||||
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Feature-specific Information Transfer scripts Resource Report Resource Website 1+ mentions |
Feature-specific Information Transfer scripts (RRID:SCR_024772) | software resource, source code | Software application as MATLAB scripts to compute measures of Feature-specific Information Transfer (FIT) and conditional FIT (cFIT). FIT quantifies direction and magnitude of information flow about specific feature S (such as feature of sensory stimulus) between simultaneously recorded brain regions X and Y. cFIT quantifies amount of directed feature information transmitted between regions X and Y that cannot be potentially routed through region Z. | MATLAB scripts, compute measures of Feature-specific Information Transfer, FIT, conditional FIT, cFIT, | European Unions Horizon 2020 Framework Programme for Research and Innovation ; NINDS U19 NS107464; NINDS R01 NS109961; NINDS R01 NS108410; Simons Foundation |
PMID:37398375 | Free, Available for download, Freely available | SCR_024772 | 2026-08-12 10:53:18 | 1 | |||||||||
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LemkeCelottoEtAl_codes_repo Resource Report Resource Website 1+ mentions |
LemkeCelottoEtAl_codes_repo (RRID:SCR_024773) | software resource, source code | Software code package associated to the paper: Lemke et al. Information flow between motor cortex and striatum reverses during skill learning. 2023. Quantifies information theoretic quantities used in the associated study. | quantifies information theoretic quantities used in associated study, package associated to paper, | Free, Available for download, Freely available | SCR_024773 | 2026-08-12 10:53:13 | 1 | |||||||||||
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CZ CELLxGENE Discover Resource Report Resource Website 100+ mentions |
CZ CELLxGENE Discover (RRID:SCR_024894) | data or information resource, database, catalog, portal | Portal used to find and download any of data sets published on CELLxGENE. Allows to download and visually explore data to understand functionality of human tissues at cellular level. Optimized for finding, exploring, and reusing single cell data. Collections Page lists collections hosted on CELLxGENE Discover and metadata that define tissue, assay, disease, organism, and cell count for each collection. Once you find published dataset of interest on CELLxGENE Discover, you can click on the explore button below the dataset description to explore the cells of that dataset using the CELLxGENE Explorer. | BICAN, visually explore data, functionality of human tissues at cellular level, tissue, assay, disease, organism, cell count, collection | is related to: BRAIN Initiative Cell Atlas Network | Free, Freely available | SCR_024894 | Chan Zuckerberg CELL by GENE Discover | 2026-08-12 10:53:15 | 139 | |||||||||
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Adobe Fresco Resource Report Resource Website 1+ mentions |
Adobe Fresco (RRID:SCR_024887) | software resource, software application | Software digital painting and drawing application. Used to create figures. Built for the latest stylus and touch devices, now including iPhones. Collection of vector and raster brushes, live brushes, to deliver natural painting and drawing experience.Vector and raster graphics editor developed by Adobe primarily for digital painting. Originally designed for the Apple iPad with Pencil support. | Adobe, collection of vector and raster brushes, live brushes, digital painting and drawing, | Restricted | SCR_024887 | 2026-08-12 10:53:13 | 1 |
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