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https://github.com/calebclayreagor/DELAY

Software application as convolutional neural network for inference of gene-regulatory relationships across pseudotime-ordered single-cell trajectories. Used for depicting pseudotime-lagged causality for accurate gene-regulatory inference.

Proper citation: DELAY (RRID:SCR_027302) Copy   

•   Source: SciCrunch Registry

https://pypi.org/project/transformers/

Software framework for machine learning models in text, computer vision, audio, video, and multimodal model, for both inference and training.

Proper citation: Transformers (RRID:SCR_027381) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/CNVMetrics/

Software R package to calculate similarity metrics to facilitate copy number variant comparison among samples and/or methods.

Proper citation: CNVMetrics (RRID:SCR_027263) Copy   

•   Source: SciCrunch Registry

https://github.com/wenmm/EssSubgraph/tree/main

A model algorithm that integrates omics data and network data to predict essential genes.

Proper citation: EssSubgraph (RRID:SCR_027354) Copy   

•   Source: SciCrunch Registry

http://www.drive5.com

Software application that provides search and clustering functionality, typically used with amplicon sequence data. Used to assign sequences to clusters.

Proper citation: USEARCH (RRID:SCR_027438) Copy   

•   Source: SciCrunch Registry

https://github.com/kermitt2/grobid

Software tool for extracting information from scholarly documents.

Proper citation: Grobid (RRID:SCR_027539) Copy   

•   Source: SciCrunch Registry

https://github.com/hejDMC/napari-dmc-brainmap

Software napari plugin for flexible mapping of various features (cell bodies, axonal densities, injections sites, optical fibers, Neuropixels probes) to standardized reference spaces included in BrainGlobe. Used for anatomical mapping.

Proper citation: DMC-BrainMap (RRID:SCR_027433) Copy   

•   Source: SciCrunch Registry

https://github.com/hejDMC/dmc-fluoimager

Software Python project for whole slide image acquisition using a fluorescence microscope.

Proper citation: DMC-FluoImager (RRID:SCR_027435) Copy   

•   Source: SciCrunch Registry

https://github.com/jmschrei/memesuite-lite

Software application as lightweight reimplementation of some of the algorithms in the MEME suite in Python.

Proper citation: memesuite-lite (RRID:SCR_027429) Copy   

•   Source: SciCrunch Registry

https://www.uhn.ca/

public research and teaching hospital network in Toronto, Ontario, Canada. It is affiliated with the Temerty Faculty of Medicine at the University of Toronto, and is the largest health research organization in Canada, ranking first in the country for total research funding.

Proper citation: University Health Network (RRID:SCR_027533) Copy   

•   Source: SciCrunch Registry

https://github.com/wheaton5/souporcell

Software tool to cluster cells using the genetic variants detected within the scRNAseq reads. Robust clustering of single-cell RNA-seq data by genotype without reference genotypes. Used for clustering scRNAseq by genotypes.

Proper citation: Souporcell (RRID:SCR_027462) Copy   

•   Source: SciCrunch Registry

https://github.com/HazyResearch/hyena-dna

Software application as long-range genomic foundation model pretrained on context lengths of up to 1 million tokens at single nucleotide resolution.

Proper citation: HyenaDNA (RRID:SCR_027471) Copy   

•   Source: SciCrunch Registry

https://github.com/MANO-B/U3-Nomogram

Software application for C-CAT CALICO database. Used for Germline-focUsed analysis of tUmoUr-detected variants with Nomogram for C-CAT CALICO database.

Proper citation: U3-Nomogram (RRID:SCR_027696) Copy   

•   Source: SciCrunch Registry

https://guolab.wchscu.cn/ImmuCellAI/#!/

Software tool for comprehensive T‐Cell subsets abundance prediction and its application in cancer immunotherapy.

Proper citation: ImmuCellAI (RRID:SCR_027645) Copy   

•   Source: SciCrunch Registry

https://atlantis.bioinfolab.sns.it

Integrative database for human proteome structural and functional sites. Used for understanding role of specific residues in protein structures, complexes, and interaction networks. Integrates various structural and functional annotation layers for each residue, offering comprehensive understanding of protein functionality.

Proper citation: Atlantis (RRID:SCR_027648) Copy   

•   Source: SciCrunch Registry

https://github.com/broadinstitute/multiVIB

Software tool as comprehensive framework for integration of single-cell omics data with probabilistic contrastive learning.

Proper citation: multiVIB (RRID:SCR_027589) Copy   

•   Source: SciCrunch Registry

https://github.com/cancerit/ClusterSV

Software application to group genetic structural variant rearrangements into rearrangement clusters and footprints. Used in the PCAWG-6 project.

Proper citation: ClusterSV (RRID:SCR_027722) Copy   

•   Source: SciCrunch Registry

https://github.com/BioDepot/SpatialProteomics

Software graphical and containerized spatial proteomics workflow. End-to-end containerized spatial proteomics analysis workflow with QuPath integration. Consists of cell segmentation, batch correction, unsupervised clustering, validation of clusters on the image, and cell type clustering results visualization.

Proper citation: SpatialProteomics (RRID:SCR_027835) Copy   

•   Source: SciCrunch Registry

https://github.com/bbglab/intogen-plus

Software tool for automatic and comprehensive knowledge extraction based on mutational data from sequenced tumor samples from patients. Summarizes somatic mutations, genes and pathways involved in tumorigenesis.

Proper citation: IntOGen (RRID:SCR_027727) Copy   

•   Source: SciCrunch Registry

https://github.com/eyzhao/hrdetect-pipeline

Software tool for detection and analysis of homologous recombination events.

Proper citation: HRDetect (RRID:SCR_027726) Copy   

•   Source: SciCrunch Registry