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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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DevATLAS Resource Report Resource Website |
DevATLAS (RRID:SCR_025718) | data or information resource, atlas, reference atlas | Whole brain developmental map of neuronal circuit maturation. Generated by whole brain spatiotemporal mapping of circuit maturation during early postnatal development. Standard reference for normative developmental trajectory of neuronal circuit maturation, as well as high throughput platform to pinpoint when and where circuit maturation is disrupted in mouse models of neurodevelopmental disorders, such as fragile X syndrome. | Whole brain developmental map, neuronal circuit maturation, whole brain spatiotemporal mapping, circuit maturation, early postnatal development, mouse models of neurodevelopmental disorders, | Human Frontier Science Program ; Brain Research Foundation Seed Grant ; Simons Center for the Social Brain Equipment Grant ; Paul and Lilah Newton Brain Science Award ; NIMH RF1MH124605; NIDCD DC014701; NINDS NS123710; NINDS NS115543; NIMH MH116673 |
PMID:38260331 | Free, Freely available | DevATLAS | SCR_025718 | Developmental Activation Timing-based Longitudinal Acquisition System | 2026-08-09 09:09:19 | 0 | |||||||
|
ElemeFE element-angular Resource Report Resource Website 1+ mentions |
ElemeFE element-angular (RRID:SCR_025725) | source code, software resource | Open-source angularjs theme. Element for Angular. | Element for Angular, angularjs theme, | Free, Available for download, Freely available | SCR_025725 | 2026-08-09 09:08:51 | 1 | |||||||||||
|
PAL:Proactive Automatized Lifestyle intervention Resource Report Resource Website |
PAL:Proactive Automatized Lifestyle intervention (RRID:SCR_025727) | software application, software resource | Behavior change intervention software. Participants enter their data as part of online survey, and software generates individualized feedback letters. | Behavior change intervention, behavior change, intervention | German Cancer Aid ; German Research Foundation ; German Ministry of Education and Research |
PMID:36123081 | Restricted | SCR_025727 | 2026-08-09 09:09:18 | 0 | |||||||||
|
MetaCycle Resource Report Resource Website 50+ mentions |
MetaCycle (RRID:SCR_025729) | software toolkit, software resource | Software R package for detecting rhythmic signals from large scale time-series data. Used to evaluate periodicity in large scale data. | detecting rhythmic signals, large scale time-series data, rhythmic signals, evaluate periodicity, large scale data, | NINDS R01NS054794; Defence Advanced Research Projects Agency |
PMID:27378304 | Free, Available for download, Freely available | https://github.com/gangwug/MetaCycle | SCR_025729 | 2026-08-09 09:09:18 | 60 | ||||||||
|
Clair3 Resource Report Resource Website 10+ mentions |
Clair3 (RRID:SCR_026063) | source code, software resource | Software tool as germline small variant caller for long-reads. Symphonizing pileup and full-alignment for high-performance long-read variant calling. | full-alignment, long-read variant calling, germline small variant caller, long-reads, variant caller, | PMID:38177392 | Free, Available for download, Freely available | SCR_026063 | 2026-08-09 09:08:56 | 28 | ||||||||||
|
rwnull / insitu_probe_generator Resource Report Resource Website 1+ mentions |
rwnull / insitu_probe_generator (RRID:SCR_025981) | source code, software resource | Code generated for use in Python to create DNA probes for use in hybridisation chain reaction, which allows for spatial resolution of mRNA expression with fluorescently tagged hairpins that bind to DNA probes. Used to generate HCR-style Probe Pairs for mRNA visualization. | generate HCR-style Probe Pairs, Probe Pairs for mRNA visualization, create DNA probes, hybridisation chain reaction, | Free, Available for download, Freely available, | SCR_025981 | 2026-08-09 09:09:21 | 1 | |||||||||||
|
q2-predict-dysbiosis Resource Report Resource Website 1+ mentions |
q2-predict-dysbiosis (RRID:SCR_026038) | Q2PD | source code, software resource | Function-based gut microbiome health index. | Function-based, gut microbiome, health index, | DOI:10.1101/2023.12.04.569909 | Free, Available for download, Freely available | SCR_026038 | 2026-08-09 09:08:56 | 1 | |||||||||
|
ArCH Resource Report Resource Website 1+ mentions |
ArCH (RRID:SCR_025975) | ArCH | software toolkit, software resource | Software somatic variant calling pipeline designed to detect low variant allele fraction clonal hematopoiesjsonsis variants. | sequencing studies analysis, somatic variant calling, detect low variant allele fraction, clonal hematopoiesjsonsis variants, | Edward P. Evans Foundation ; American Society of Hematology ; NCI K08 CA241318; NCI P30 CA008748 |
PMID:38485690 | Free, Available for download, Freely available, | SCR_025975 | , ArCH: Artifact Filtering Clonal Hematopoiesis Variant Calling Pipeline, Artifact Filtering Clonal Hematopoiesis Variant Calling Pipeline | 2026-08-09 09:09:21 | 1 | |||||||
|
STdeconvolve Resource Report Resource Website 1+ mentions |
STdeconvolve (RRID:SCR_025977) | software toolkit, software resource | Software R package as unsupervised, reference-free approach to infer latent cell-type proportions and transcriptional profiles within multi-cellular spatially-resolved pixels from spatial transcriptomics datasets. | infer latent cell-type proportions and transcriptional profiles, infer latent cell-type proportions, transcriptional profiles, | Free, Freely available | SCR_025977 | 2026-08-09 09:09:21 | 2 | |||||||||||
|
PythonVideoAnnotator Resource Report Resource Website 1+ mentions |
PythonVideoAnnotator (RRID:SCR_025868) | software application, software resource | Software graphical application written in Python, to analyze videos and create notes for events in the video. Used to identify animals’ behaviors based on information extracted from video. | graphical application, analyze videos, create notes, identify animals’ behaviors, | Free, Freely available | SCR_025868 | 2026-08-09 09:08:54 | 1 | |||||||||||
|
MySQL-server Resource Report Resource Website 1+ mentions |
MySQL-server (RRID:SCR_025972) | source code, software resource | Open source Relational Database Management System that enables users to store, manage, and retrieve structured data efficiently. | SQL, relational database management system, Structured Query Language Server, | Free, Available for download, Freely available | SCR_025972 | My Structured Query Language Server | 2026-08-09 09:09:21 | 2 | ||||||||||
|
STAR-Fusion Resource Report Resource Website 10+ mentions |
STAR-Fusion (RRID:SCR_025853) | source code, software resource | Software tool to leverage chimeric and discordant read alignments identified by STAR aligner to predict fusions. Component of Trinity Cancer Transcriptome Analysis Toolkit. Used to identify candidate fusion transcripts supported by Illumina reads. Maps junction reads and spanning reads to reference annotation set. | identify candidate fusion transcripts, predict fusions, leverages chimeric and discordant read alignments, chimeric, discordant, read alignment, | Howard Hughes Medical Institute ; Klarman Cell Observatory ; NCI U24CA180922; NCI R50CA211461; NCI R21CA209940; NCI U01CA214846 |
PMID:31639029 | Free, Available for download, Freely available | SCR_025853 | 2026-08-09 09:09:20 | 47 | |||||||||
|
pracma Resource Report Resource Website 1+ mentions |
pracma (RRID:SCR_026021) | software toolkit, software resource | Software R package provides functions from numerical analysis and linear algebra, numerical optimization, differential equations, time series, plus some well-known special mathematical functions. Uses 'MATLAB' function names where appropriate to simplify porting. | R, numerical analysis functions, linear algebra functions, numerical optimization, differential equations, time series, | Free, Available for download, Freely available | SCR_026021 | Practical Numerical Math Functions, pracma: Practical Numerical Math Functions | 2026-08-09 09:09:22 | 9 | ||||||||||
|
MethylSig Resource Report Resource Website 1+ mentions |
MethylSig (RRID:SCR_025849) | software toolkit, software resource | Software R package as whole genome DNA methylation analysis pipeline. Used for testing differentially methylated cytosines or regions in whole-genome bisulfite sequencing or reduced representation bisulfite sequencing experiments. Several options exist for either site-specific or sliding window tests, and variance estimation. | whole genome DNA methylation analysis, whole genome DNA, DNA methylation, testing differentially methylated cytosines, whole-genome bisulfite sequencing, reduced representation bisulfite sequencing, | NCI R01CA158286; NIEHS P30 ES017885 |
PMID:24836530 | Free, Available for download, Freely available | SCR_025849 | 2026-08-09 09:08:53 | 3 | |||||||||
|
ZetaStitcher Resource Report Resource Website 10+ mentions |
ZetaStitcher (RRID:SCR_026193) | source code, software resource | Software tool designed to stitch large volumetric images such as those produced by Light-Sheet Fluorescence Microscopes. | Light-Sheet Fluorescence Microscopes, Light-Sheet Fluorescence Microscopes images, stitch large volumetric images, | European Union Horizon 2020 Framework Programme for Research and Innovation | Free, Available for download, Freely available | SCR_026193 | 2026-08-09 09:09:23 | 12 | ||||||||||
|
spatial_tri-omics Resource Report Resource Website 1+ mentions |
spatial_tri-omics (RRID:SCR_026194) | source code, software resource | Software repository to share the raw data processing and visualization codes used in the spatial tri-omics project. | raw data processing and visualization codes, spatial tri-omics project, | Free, Available for download, Freely available | SCR_026194 | 2026-08-09 09:08:59 | 2 | |||||||||||
|
AutoPVS Resource Report Resource Website |
AutoPVS (RRID:SCR_026108) | software application, software resource | Software automatic classification tool for PVS1 interpretation of null variants. | automatic classification, PVS1 interpretation, null variants, | PMID:32442321 | Free, Available for download, Freely available | https://github.com/JiguangPeng/autopvs1 | SCR_026108 | , Automatic PVS1 interpretation, AutoPVS1 | 2026-08-09 09:09:23 | 0 | ||||||||
|
VirtualDub Resource Report Resource Website 10+ mentions |
VirtualDub (RRID:SCR_026123) | software application, software resource | Open-source software for video capture and video processing for Microsoft Windows. Designed to process linear video streams, including filtering and recompression. It uses AVI container format to store captured video. Video capture/processing utility for 32-bit and 64-bit Windows platforms. Used for processing AVI files, although it can read (not write) MPEG-1 and also handle sets of BMP images. | video capture, video processing, process linear video streams, filtering, recompression, processing AVI files, | Free, Available for download, Freely available | https://sourceforge.net/projects/virtualdub/files/ | SCR_026123 | 2026-08-09 09:08:58 | 19 | ||||||||||
|
HVSeeker Resource Report Resource Website 1+ mentions |
HVSeeker (RRID:SCR_026120) | software application, software resource | Software tool for distinguishing between bacterial and phage sequences. Consists of two separate models: one analyzing DNA sequences and the other focusing on proteins. | genome, bacteria, phage, sequence, distinguishing between bacterial and phage sequences, | German Research Foundation INST 37/935-1 FUGG; King Fahd University of Petroleum and Minerals |
Free, Available for download, Freely available, | SCR_026120 | 2026-08-09 09:08:58 | 1 | ||||||||||
|
Global Environment Facility Resource Report Resource Website |
Global Environment Facility (RRID:SCR_026241) | nonprofit organization, funding resource | Provides information about family of funds for the environment. With GEF support,countries address the root causes of challenges as they strive for international environmental goals. Fund data from the Global Environment Facility. | funds for environment, international environmental goals, | SCR_026241 | 2026-08-09 09:09:24 | 0 |
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