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https://github.com/open2c/cooltools

Software suite of computational tools that enables flexible, scalable, and reproducible analysis of high-resolution contact frequency data. Provides suite of computational tools with paired python API and command line access, which facilitates workflows either on high-performance computing clusters or via custom analysis notebooks. As part of the Open2C ecosystem, cooltools also provides detailed introductions to key concepts in Hi-C-data analysis with interactive notebook documentation.

Proper citation: cooltools (RRID:SCR_026118) Copy   

•   Source: SciCrunch Registry

https://genie.cbioportal.org/

International data-sharing consortium focused on generating an evidence base for precision cancer medicine by integrating clinical-grade cancer genomic data with clinical outcome data of cancer patients treated at multiple institutions worldwide.

Proper citation: AACR GENIE cBioPortal (RRID:SCR_026217) Copy   

•   Source: SciCrunch Registry

https://github.com/huangnengCSU/compleasm

Software genome completeness evaluation tool based on miniprot.

Proper citation: compleasm (RRID:SCR_026370) Copy   

•   Source: SciCrunch Registry

https://github.com/WGLab/LongReadSum

Software fast and flexible QC and signal summarization tool for long read sequencing data.

Proper citation: LongReadSum (RRID:SCR_026408) Copy   

•   Source: SciCrunch Registry

https://gkb.dcmb.med.umich.edu

Database that uses knowledge graph to consolidate genomic datasets and annotations. Graph database for researchers to explore and investigate human genome, epigenome, transcriptome, and 4D nucleome. Genomic entities and relationships are represented as diverse nodes and edges with properties.

Proper citation: GenomicKB (RRID:SCR_026591) Copy   

•   Source: SciCrunch Registry

https://github.com/GreenleafLab/chromVAR

Software R package for analyzing sparse chromatin-accessibility data by estimating gain or loss of accessibility within peaks sharing the same motif or annotation while controlling for technical biases. Enables accurate clustering of scATAC-seq profiles and characterization of known and de novo sequence motifs associated with variation in chromatin accessibility. Used for analysis of sparse chromatin accessibility data from single cell or bulk ATAC or DNAse-seq data.

Proper citation: chromvar (RRID:SCR_026570) Copy   

•   Source: SciCrunch Registry

https://github.com/QuackenbushLab/NetworkDataCompanion

Software R library of utilities for performing analyses on TCGA and GTEx data using the Network Zoo. Streamlines routine steps in TCGA data processing, including filtering and mapping gene and sample identifiers between modalities and allows modality-specific data transformation, such as normalization and cleaning.

Proper citation: NetworkDataCompanion (RRID:SCR_026532) Copy   

•   Source: SciCrunch Registry

https://github.com/jackh726/bigtools

Software library and associated tools for reading and writing bigwig and bigbed files. High-performance BigWig and BigBed library in Rust.

Proper citation: Bigtools (RRID:SCR_026627) Copy   

•   Source: SciCrunch Registry

https://github.com/calico/borzoi

Software package to access the Borzoi models, which are convolutional neural networks trained to predict RNA-seq coverage at 32bp resolution given 524kb input sequences.

Proper citation: Borzoi (RRID:SCR_026619) Copy   

•   Source: SciCrunch Registry

https://scvi-tools.org/

Software Python library for deep probabilistic analysis of single-cell and spatial omics data. Used for probabilistic modeling and analysis of single-cell omics data, built on top of PyTorch and AnnData.

Proper citation: scvi-tools (RRID:SCR_026673) Copy   

•   Source: SciCrunch Registry

https://github.com/AfriGen-D/Phenotype_Collection_Toolkits

Software suite of data collection toolkits that cover range of biomedical research fields. These toolkits provide data collection forms that can be used to build research database and can facilitate phenotype standardisation and harmonisation efforts on African continent and larger user community.

Proper citation: Phenotype Data Collection Toolkits (RRID:SCR_026924) Copy   

•   Source: SciCrunch Registry

https://github.com/slowkoni/rfmix

Software tool for local ancestry and admixture inference. Discriminative Modeling Approach for Rapid and Robust Local-Ancestry Inference.

Proper citation: RFMix (RRID:SCR_027030) Copy   

•   Source: SciCrunch Registry

https://seahorse.networkmedicine.org

Web-based database and search tool for exploratory data analysis in which we have pre-computed statistical associations between available data elements. Large-scale, open-access data sets such as the Genotype Tissue Expression Project (GTEx) and The Cancer Genome Atlas (TCGA) include multi-omic data on large numbers of samples along with extensive clinical and phenotypic information. Allows users to explore significant associations using tabulated summary statistics, data visualizations, and functional enrichment analyses (using RNA-seq data) for identified sets of genes.

Proper citation: SEAHORSE (RRID:SCR_027399) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/release/bioc/html/GenVisR.html

Software R package for visualizing genomics data. Provides a user-friendly, flexible and comprehensive suite of tools for visualizing complex genomic data in three categories (small variants, copy number alterations and data quality) for multiple species of interest.

Proper citation: GenVisR (RRID:SCR_027559) Copy   

•   Source: SciCrunch Registry

https://github.com/Danko-Lab/BayesPrism

Software R package for fully Bayesian inference of tumor microenvironment composition and gene expression deconvolution. Used to analyze bulk RNA-seq data and estimate cell type-specific expression profiles.

Proper citation: BayesPrism (RRID:SCR_027499) Copy   

•   Source: SciCrunch Registry