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https://github.com/rwnull/insitu_probe_generator?tab=readme-ov-file

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.

Proper citation: rwnull / insitu_probe_generator (RRID:SCR_025981) Copy   

•   Source: SciCrunch Registry

https://github.com/Kizielins/q2-predict-dysbiosis/tree/master

Function-based gut microbiome health index.

Proper citation: q2-predict-dysbiosis (RRID:SCR_026038) Copy   

•   Source: SciCrunch Registry

https://github.com/kbolton-lab/ArCH

Software somatic variant calling pipeline designed to detect low variant allele fraction clonal hematopoiesjsonsis variants.

Proper citation: ArCH (RRID:SCR_025975) Copy   

•   Source: SciCrunch Registry

https://www.bioconductor.org/packages/release/bioc/html/STdeconvolve.html

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.

Proper citation: STdeconvolve (RRID:SCR_025977) Copy   

•   Source: SciCrunch Registry

https://pythonvideoannotator.readthedocs.io/en/master/index.html

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.

Proper citation: PythonVideoAnnotator (RRID:SCR_025868) Copy   

•   Source: SciCrunch Registry

https://github.com/mysql/mysql-server

Open source Relational Database Management System that enables users to store, manage, and retrieve structured data efficiently.

Proper citation: MySQL-server (RRID:SCR_025972) Copy   

•   Source: SciCrunch Registry

https://github.com/STAR-Fusion/STAR-Fusion

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.

Proper citation: STAR-Fusion (RRID:SCR_025853) Copy   

•   Source: SciCrunch Registry

https://CRAN.R-project.org/package=pracma

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.

Proper citation: pracma (RRID:SCR_026021) Copy   

•   Source: SciCrunch Registry

https://www.bioconductor.org/packages/release/bioc/html/methylSig.html

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.

Proper citation: MethylSig (RRID:SCR_025849) Copy   

•   Source: SciCrunch Registry

https://github.com/lens-biophotonics/ZetaStitcher

Software tool designed to stitch large volumetric images such as those produced by Light-Sheet Fluorescence Microscopes.

Proper citation: ZetaStitcher (RRID:SCR_026193) Copy   

•   Source: SciCrunch Registry

https://github.com/di-0579/spatial_tri-omics

Software repository to share the raw data processing and visualization codes used in the spatial tri-omics project.

Proper citation: spatial_tri-omics (RRID:SCR_026194) Copy   

•   Source: SciCrunch Registry

https://autopvs1.bgi.com/

Software automatic classification tool for PVS1 interpretation of null variants.

Proper citation: AutoPVS (RRID:SCR_026108) Copy   

•   Source: SciCrunch Registry

https://www.virtualdub.org

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.

Proper citation: VirtualDub (RRID:SCR_026123) Copy   

•   Source: SciCrunch Registry

https://github.com/BackofenLab/HVSeeker/tree/main

Software tool for distinguishing between bacterial and phage sequences. Consists of two separate models: one analyzing DNA sequences and the other focusing on proteins.

Proper citation: HVSeeker (RRID:SCR_026120) Copy   

•   Source: SciCrunch Registry

https://www.thegef.org/projects-operations/recipient-countries/

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.

Proper citation: Global Environment Facility (RRID:SCR_026241) Copy   

•   Source: SciCrunch Registry

https://akoyabio.github.io/phenoptr/index.html

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.

Proper citation: phenoptr (RRID:SCR_026104) Copy   

•   Source: SciCrunch Registry

https://winscp.net/eng/download.php

Free file manager, SSH File Transfer Protocol, File Transfer Protocol, WebDAV, Amazon S3, and secure copy protocol client for Microsoft Windows.

Proper citation: WinSCP (RRID:SCR_026226) Copy   

•   Source: SciCrunch Registry

https://github.com/ganlab/GALA

Softawer framework for de novo chromosome-by-chromosome assembly with long reads. Long-reads gap-free chromosome-scale assembler.

Proper citation: GALA (RRID:SCR_026184) Copy   

•   Source: SciCrunch Registry

https://CRAN.R-project.org/package=optmatch

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.

Proper citation: optmatch (RRID:SCR_026185) Copy   

•   Source: SciCrunch Registry

https://github.com/dpeerlab/ENVI

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.

Proper citation: ENVI (RRID:SCR_026160) Copy   

•   Source: SciCrunch Registry