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https://github.com/davidemms/OrthoFinder

Software Python application for comparative genomics analysis. Finds orthogroups and orthologs, infers rooted gene trees for all orthogroups and identifies all of gene duplcation events in those gene trees, infers rooted species tree for species being analysed and maps gene duplication events from gene trees to branches in species tree, improves orthogroup inference accuracy. Runs set of protein sequence files, one per species, in FASTA format.

Proper citation: OrthoFinder (RRID:SCR_017118) Copy   

•   Source: SciCrunch Registry

http://phaffcollection.ucdavis.edu/

Collection of wild yeast in the world. Academic and industrial resarchers utilize this collection for a variety of research and applications, including pigments, enzymes, food ingredients, and hosts for protein expression. Provides contract screening and strain selection services.

Proper citation: Phaff Yeast Culture Collection (RRID:SCR_016781) Copy   

•   Source: SciCrunch Registry

https://github.com/mikelove/tximport

Software R package for importing pseudoaligned reads into R for use with downstream differential expression analysis. Used for import and summarize transcript level estimates for transcript and gene level analysis.

Proper citation: tximport (RRID:SCR_016752) Copy   

•   Source: SciCrunch Registry

https://nephele.niaid.nih.gov

Cloud based platform for simplified, standardized and reproducible microbiome data analysis. Allows users to process microbiome datasets through pipelines of existing software tools.

Proper citation: Nephele (RRID:SCR_016595) Copy   

•   Source: SciCrunch Registry

https://github.com/theislab/scanpy

Software Python tool for large scale single cell gene expression data analysis. Integrates analysis possibilities of established R-based frameworks, provides pre processing, visualization, graph-drawing and diffusion maps, clustering, identification of marker genes for clusters via differential expression tests and pseudo temporal ordering via diffusion pseudo time.

Proper citation: scanpy (RRID:SCR_018139) Copy   

•   Source: SciCrunch Registry

http://pixelink.com/home/products/software/drivers/

Software application for real-time, interactive, multi-camera recording. It is compatible with all Pixelink PL-B and PL-D line of cameras.

Proper citation: Pixelink Image Capture Software (RRID:SCR_016197) Copy   

•   Source: SciCrunch Registry

https://cgb.indiana.edu

CGB offers range of genomic services, including high-throughput DNA/RNA extraction, library preparation, next-generation sequencing, and bioinformatic analysis.

Proper citation: Indiana University Center for Genomics and Bioinformatics Core Facility (RRID:SCR_017165) Copy   

•   Source: SciCrunch Registry

https://www.ncbi.nlm.nih.gov/labs/virus/vssi

Community portal for viral sequence data from RefSeq, GenBank and other NCBI repositories. Integrative, value added resource designed to support retrieval, display and analysis of curated collection of virus sequences and large sequence datasets. Used to increase usability of data archived in GenBank and other NCBI repositories.

Proper citation: NCBI Virus (RRID:SCR_018253) Copy   

•   Source: SciCrunch Registry

https://tmcalculator.neb.com/#!/main

Calculator to estimate appropriate annealing temperature when using NEB PCR products.Tm calculator provided by New England Biolabs.

Proper citation: NEB Tm calculator (RRID:SCR_017969) Copy   

•   Source: SciCrunch Registry

https://www.ncbi.nlm.nih.gov/sutils/pasc/viridty.cgi

Web tool for analysis of pairwise identity distribution within viral families. Used for virus sequence-based classification. Data in the system are updated every day to reflect changes in virus taxonomy and additions of new virus sequences to the public database.

Proper citation: PASC (RRID:SCR_016642) Copy   

•   Source: SciCrunch Registry

https://github.com/zburkett/VoICE

Software that groups vocal elements of birdsong by creating a high dimensionality dataset through scoring spectral similarity between vocalizations.

Proper citation: Vocal Inventory Clustering Engine (VoICE) (RRID:SCR_016004) Copy   

•   Source: SciCrunch Registry

https://singularityhub.github.io/sregistry

Web application and registry for institutional deployment of Singularity containers.

Proper citation: Singularity Registry (RRID:SCR_016249) Copy   

•   Source: SciCrunch Registry

http://ccg.vital-it.ch/snp2tfbs

Collection of text files providing specific annotations for human single nucleotide polymorphisms (SNPs), namely whether they are predicted to abolish, create or change the affinity of one or several transcription factor (TF) binding sites. Used to investigate the molecular mechanisms underlying regulatory variation in the human genome. SNP2TFBS is also accessible over a web interface, enabling users to view the information provided for an individual SNP, to extract SNPs based on various search criteria, to annotate uploaded sets of SNPs or to display statistics about the frequencies of binding sites affected by selected SNPs.

Proper citation: SNP2TFBS (RRID:SCR_016885) Copy   

•   Source: SciCrunch Registry

https://www.hopkinsmedicine.org/institute-basic-biomedical-sciences/services/single-cell-sequencing-transcriptomics-core

Core provides assistance with Single Cell RNA and DNA Sequencing, Spatial Transcriptomics, Next-Generation Sequencing libraries.

Proper citation: Johns Hopkins Medicine Institute for Basic Biomedical Sciences Single Cell and Transcriptomics Core Facility (RRID:SCR_017172) Copy   

•   Source: SciCrunch Registry

http://hpc-bioinformatics.cineca.it/stress_mice/

Sapienza University of Rome and Cineca consortium portal. Used for analyzing published RNAseq transcriptomes obtained from brain of mice exposed to different kinds of stress protocols, to generate database of stress related differentially expressed genes and to identify factors contributing to vulnerability or resistance to stress. Allows to query database of RNAseq data.

Proper citation: Stress Mice Portal (RRID:SCR_017572) Copy   

•   Source: SciCrunch Registry

https://github.com/broadinstitute/Drop-seq

Software Java tools for analyzing Drop-seq data. Used to analyze gene expression from thousands of individual cells simultaneously. Analyzes mRNA transcripts while remembering origin cell transcript.

Proper citation: Drop-seq tools (RRID:SCR_018142) Copy   

•   Source: SciCrunch Registry

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

Software package to assess cell type identity using both functional and random gene sets. Used for single cell replicability analysis to quantify cell type replicability across datasets using neighbor voting.

Proper citation: MetaNeighbor (RRID:SCR_016727) Copy   

•   Source: SciCrunch Registry

https://omicc.niaid.nih.gov

Community based, biologist friendly web platform for creating and meta analyzing annotated gene expression data compendia., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: OMiCC (RRID:SCR_016604) Copy   

•   Source: SciCrunch Registry

http://asaim.readthedocs.io

Software that analyzes intestinal microbiota data. This environment is composed of a framework to process and analyze microbiota data from raw sequences to taxonomic and functional assignations.

Proper citation: ASaiM (RRID:SCR_015878) Copy   

•   Source: SciCrunch Registry

https://github.com/wilkinsonlab/epigenomics_pipeline

Software tool as epigenomics analysis pipeline for analysis of ChIP-Seq and RNA-Seq data using Docker images containing Galaxy and Jupyter.

Proper citation: Epigenomics Workflow on Galaxy and Jupyter (RRID:SCR_017544) Copy   

•   Source: SciCrunch Registry