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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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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 | |||||||||||
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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 | |||||||||
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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 | |||||||
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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 | |||||||||||
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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 | |||||||||||
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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 | ||||||||||
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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 | |||||||||
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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 | ||||||||||
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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 | |||||||||
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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 | ||||||||||
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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 | |||||||||||
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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 | ||||||||
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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 | ||||||||||
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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 | ||||||||||
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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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phenoptr Resource Report Resource Website 1+ mentions |
phenoptr (RRID:SCR_026104) | source code, software resource | Software R package for working with inForm data. Contains functions that make it easier to read and analyze data tables and images created by Akoya Biosciences' inForm software. | read data, analyze data, tables and images, Akoya Biosciences, inForm | Free, Available for download, Freely available, | https://github.com/akoyabio/phenoptr | SCR_026104 | 2026-08-09 09:09:23 | 8 | ||||||||||
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WinSCP Resource Report Resource Website 1+ mentions |
WinSCP (RRID:SCR_026226) | software application, software resource | Free file manager, SSH File Transfer Protocol, File Transfer Protocol, WebDAV, Amazon S3, and secure copy protocol client for Microsoft Windows. | file manager, SSH File Transfer Protocol, File Transfer Protocol, WebDAV, Amazon S3, secure copy protocol client, Microsoft Windows, | Free, Available for download, Freely available | SCR_026226 | 2026-08-09 09:09:00 | 5 | |||||||||||
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GALA Resource Report Resource Website 1+ mentions |
GALA (RRID:SCR_026184) | GALA | source code, software resource | Softawer framework for de novo chromosome-by-chromosome assembly with long reads. Long-reads gap-free chromosome-scale assembler. | long-reads gap-free chromosome-scale assembler | PMID:36639368 | Free, Available for download, Freely available | SCR_026184 | GAp-free Long-read Assembler | 2026-08-09 09:09:24 | 1 | ||||||||
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optmatch Resource Report Resource Website 1+ mentions |
optmatch (RRID:SCR_026185) | software toolkit, software resource | Software package for optimal matching in R. Distance based bipartite matching using minimum cost flow, oriented to matching of treatment and control groups in observational studies. Routines are provided to generate distances from generalised linear models (propensity score matching), formulas giving variables on which to limit matched distances, stratified or exact matching directives, or calipers, alone or in combination. | Distance based bipartite matching, optimal matching in R, matching of treatment and control groups in observational studies, | DOI:10.1198/106186006X137047 | Free, Available for download, Freely available | https://github.com/markmfredrickson/optmatch | SCR_026185 | 2026-08-09 09:09:23 | 3 | |||||||||
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ENVI Resource Report Resource Website 1+ mentions |
ENVI (RRID:SCR_026160) | source code, software resource | Deep learnining based variational inference method to integrate scRNA-seq with spatial transcriptomics data. ENVI learns to reconstruct spatial onto for dissociated scRNA-seq data and impute unimagd genes onto spatial data. | integrate scRNA-seq with spatial transcriptomics data, integrate, scRNA-seq data, unimagd genes, | Free, Available for download, Freely available | SCR_026160 | 2026-08-09 09:09:24 | 1 |
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