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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://www.wuxiapptec.com/services/

Pharmaceutical, biopharmaceutical, and medical device company founded in December 2000 in Shanghai. Contract research organization.

Proper citation: Wuxi AppTec (RRID:SCR_026235) 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://github.com/maia-sh/aactr

Software R client for the Aggregate Content of ClinicalTrials.gov (AACT) database API.

Proper citation: aactr (RRID:SCR_026245) 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://www.alfacytology.com/cancer-modeling-services.html

Biotechnology company specialized in innovative solutions for cancer research. Provides Cancer Modeling Services to accelerate cancer therapeutics discovery and development. Contract research organization that specializes in early discovery and preclinical studies and provides cancer diagnostic biomarker development services.

Proper citation: Alfa Cytology (RRID:SCR_026128) Copy   

•   Source: SciCrunch Registry

https://github.com/openMetadataInitiative/openMINDS_chemicals

Software repository hosts one of the metadata models of the openMINDS metadata framework. It defines modular metadata schemas for describing chemical substances and mixtures.

Proper citation: openMINDS chemicals metadata model (RRID:SCR_026248) 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://github.com/18parkky/NanoMnT

Software Python package for correcting sequencing errors within Short Tandem Repeat regions from Oxford Nanopore (ONT) sequencing data and genotyping monoallelic STR regions.

Proper citation: NanoMnT (RRID:SCR_026210) 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://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

https://chempartner.com/

Life sciences contract research organization. Provides integrated life science services for drug discovery with expertise in chemistry, biology and pharmacology, DMPK, and exploratory toxicology as well as biologics discovery.

Proper citation: ChemPartner (RRID:SCR_026139) Copy   

•   Source: SciCrunch Registry

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

Software package implements method to deal with missing data. The package creates multiple imputations (replacement values) for multivariate missing data.Various diagnostic plots are available to inspect the quality of the imputations.

Proper citation: mice (RRID:SCR_026363) Copy   

•   Source: SciCrunch Registry

https://github.com/vgl-hub/gfastats

Standalone tool to compute assembly summary statistics and manipulate assembly sequences in FASTA, FASTQ or GFA [.gz] format. Gfastats stores assembly sequences internally in a GFA-like format. This feature allows gfastats to seamlessly convert FAST* to and from GFA [.gz] files. Gfastats can also build an assembly graph that can in turn be used to manipulate the underlying sequences following instructions provided by the user, while simultaneously generating key metrics for the new sequences.

Proper citation: gfastats (RRID:SCR_026368) Copy   

•   Source: SciCrunch Registry