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https://github.com/bmvdgeijn/WASP/

Software allele-specific pipeline for unbiased read mapping and molecular QTL discovery. Allele-specific software for robust molecular quantitative trait locus discovery.

Proper citation: WASP (RRID:SCR_025497) Copy   

•   Source: SciCrunch Registry

https://phenodb.org/

Database for phenotype genotype associations for humans. Used by clinical researchers to store standardized phenotypic information, diagnosis, and pedigree data and then run analyses on VCF files from individuals, families or cohorts with suspected Mendelian disease.

Proper citation: PhenoDB (RRID:SCR_016551) Copy   

•   Source: SciCrunch Registry

http://hb.flatironinstitute.org/

Formerly known as GIANT (Genome-scale Integrated Analysis of gene Networks in Tissues), HumanBase applies machine learning algorithms to learn biological associations from massive genomic data collections. These integrative analyses reach beyond existing "biological knowledge" represented in the literature to identify novel, data-driven associations.

Proper citation: HumanBase (RRID:SCR_016145) Copy   

•   Source: SciCrunch Registry

http://thecellmap.org

Web accessible database for visualizing and mining global yeast genetic interaction network. Allows users to easily access, visualize, explore, and functionally annotate genetic interactions, or to extract and reorganize sub networks, using data driven network layouts in intuitive and interactive manner. Used for storing and visualizing genetic interactions in S. cerevisiae.

Proper citation: TheCellMap (RRID:SCR_018728) Copy   

•   Source: SciCrunch Registry

http://www.regulomedb.org/

Database that annotates SNPs with known and predicted regulatory elements in intergenic regions of H. sapiens genome. Known and predicted regulatory DNA elements include regions of DNAase hypersensitivity, binding sites of transcription factors, and promoter regions that have been biochemically characterized to regulation transcription. Source of these data include public datasets from GEO, ENCODE project, and published literature.

Proper citation: RegulomeDB (RRID:SCR_017905) Copy   

•   Source: SciCrunch Registry

https://dfam.org/home

Open collection of Transposable Element DNA sequence alignments, hidden Markov Models, consensus sequences, and genome annotations.Dfam 3.2 provides early access to uncurated, de novo generated families.

Proper citation: Dfam (RRID:SCR_021168) Copy   

•   Source: SciCrunch Registry

http://clovr.org/

A desktop application for push-button automated sequence analysis that can utilize cloud computing resources. CloVR is implemented as a single portable virtual machine (VM) that provides several automated analysis pipelines for microbial genomics, including 16S, whole genome and metagenome sequence analysis. The CloVR VM runs on a personal computer, utilizes local computer resources and requires minimal installation, addressing key challenges in deploying bioinformatics workflows. In addition CloVR supports use of remote cloud computing resources to improve performance for large-scale sequence processing.

Proper citation: CloVR (RRID:SCR_005290) Copy   

•   Source: SciCrunch Registry

https://jackbibby1.github.io/SCPA/

Software R package for pathway analysis in scRNA-seq data. It’s a different approach to pathway analysis that defines pathway activity as a change in multivariate distribution of a given pathway across conditions, rather than enrichment or over representation of genes.

Proper citation: Single Cell Pathway Analysis (RRID:SCR_024909) Copy   

•   Source: SciCrunch Registry

https://github.com/hms-dbmi/UpSetR

Software R package for visualization of intersecting sets and their properties.

Proper citation: UpSetR (RRID:SCR_026112) Copy   

•   Source: SciCrunch Registry

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://github.com/czc/nb_distribution

Software tool to discover somatic and germline structural variation breakpoints in whole genome sequencing data. Can report accurate breakpoints of Deletions, Duplications, Inversions and Translocations. Designed for Illumina paired-end data. Local assembly for breakpoint detection in cancer genomes.

Proper citation: NovoBreak (RRID:SCR_026032) Copy   

•   Source: SciCrunch Registry

https://github.com/grenaud/SAFARI

C++ software program for alignment of ancient DNA to a pangenome reference graph. Used to recover more alignments from ancient DNA samples, which suffer from characteristic substitution patterns due to chemical damage.

Proper citation: SAFARI (RRID:SCR_026028) 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/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/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/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/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/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