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https://github.com/christopher-vollmers/C3POa

Software to detect DNA splint sequence raw reads. Computational pipeline for calling consensi on R2C2 nanopore data.

Proper citation: C3Poa (RRID:SCR_025484) Copy   

•   Source: SciCrunch Registry

https://github.com/bioinform/somaticseq

Software accurate somatic mutation detection pipeline implementing stochastic boosting algorithm to produce somatic mutation calls for both single nucleotide variants and small insertions and deletions. NGS variant calling and classification.

Proper citation: SomaticSeq (RRID:SCR_024891) Copy   

•   Source: SciCrunch Registry

https://pephub.databio.org

Web biological metadata server to view, store, and share your sample metadata in form of Portable Encapsulated Projects. PEPhub takes advantage of PEP biological metadata standard to store, edit, and access your PEPs in one place. Components include database where PEPs are stored; API to programmatically read and write PEPs in database; web based user interface to view and manage these PEPs via front end.

Proper citation: PEPhub (RRID:SCR_024892) Copy   

•   Source: SciCrunch Registry

https://github.com/xinhe-lab/GSFA

Software R package that performs sparse factor analysis and differential gene expression discovery simultaneously on single cell CRISPR screening data.

Proper citation: Guided Sparse Factor Analysis (RRID:SCR_025023) Copy   

•   Source: SciCrunch Registry

https://github.com/YingMa0107/CARD/

Software R package for spatial transcriptomics. Deconvolution method that combines cell-type-specific expression information from single-cell RNA sequencing (scRNA-seq) with correlation in cell-type composition across tissue locations.

Proper citation: Conditional AutoRegressive Deconvolution (RRID:SCR_026310) Copy   

•   Source: SciCrunch Registry

https://github.com/kaizhang/SnapATAC2

Software Python/Rust package for single-cell epigenomics analysis.

Proper citation: SnapATAC2 (RRID:SCR_026622) Copy   

•   Source: SciCrunch Registry

https://github.com/higlass/higlass

Web-based visual exploration and analysis of genome interaction maps.

Proper citation: HiGlass (RRID:SCR_026687) Copy   

•   Source: SciCrunch Registry

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

Software package provides Bayesian shrinkage estimators for effect sizes for variety of GLM models, using approximation of posterior for individual coefficients.

Proper citation: apeglm (RRID:SCR_026951) Copy   

•   Source: SciCrunch Registry

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

Software tool for detecting regulatory elements using GRO-seq and PRO-seq.

Proper citation: dREG (RRID:SCR_027012) Copy   

•   Source: SciCrunch Registry

https://github.com/KrishnaswamyLab/PHATE

Software tool for visualizing high dimensional data using novel conceptual framework for learning and visualizing manifold to preserve both local and global distances.

Proper citation: PHATE (RRID:SCR_027119) Copy   

•   Source: SciCrunch Registry

http://ccb.jhu.edu/software/ASprofile/

A suite of programs for extracting, quantifying and comparing alternative splicing (AS) events from RNA-seq data.

Proper citation: ASprofile (RRID:SCR_001833) Copy   

•   Source: SciCrunch Registry

http://compgen.bscb.cornell.edu/phast/

A freely available software package for comparative and evolutionary genomics that consists of about half a dozen major programs, plus more than a dozen utilities for manipulating sequence alignments, phylogenetic trees, and genomic annotations. For the most part, PHAST focuses on two kinds of applications: the identification of novel functional elements, including protein-coding exons and evolutionarily conserved sequences; and statistical phylogenetic modeling, including estimation of model parameters, detection of signatures of selection, and reconstruction of ancestral sequences. It consists of over 60,000 lines of C code.

Proper citation: PHAST (RRID:SCR_003204) Copy   

•   Source: SciCrunch Registry

http://www.phrap.org/consed/consed.html

A graphical tool for sequence finishing (BAM File Viewer, Assembly Editor, Autofinish, Autoreport, Autoedit, and Align Reads To Reference Sequence)

Proper citation: Consed (RRID:SCR_005650) Copy   

•   Source: SciCrunch Registry

https://www.phenx.org/Default.aspx?tabid=56

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on 05 01 2025. PhenX is a project to prioritize Phenotype and eXposure measures for Genome-wide Association Studies (GWAS). Leaders of the scientific community will assess and prioritize a broad range of domains relevant to genomics research and public health. The PhenX Steering Committee (SC), chaired by Dr. Jonathan Haines, provides leadership in the selection of domains and domain experts. Members of the SC include outstanding scientists from the research community and liaisons from the Institutes and Centers of the National Institutes of Health. Consensus measures for GWAS will have a direct impact on biomedical research and ultimately on public health. During the course of this project, up to 20 research domains will be examined, with up to 15 measures being recommended for use in future GWAS and other large-scale genomic research efforts. The goal is to maximize the benefits of future research by having comparable measures so that studies can be integrated. Each selected domain will be reviewed by a Working Group (WG) of scientists who are experts in the research area. A systematic review of the literature will guide the WGs selection of up to 15 high priority measures with standardized approaches for measurement. Selection criteria for the measures include factors such as validity, reproducibility, cost, feasibility, and burden to both investigators and participants. The scientific community will be asked to provide input on proposed measures. Consensus development is a key component of the project.

Proper citation: Consensus Measures for Phenotype and Exposure (RRID:SCR_006688) Copy   

•   Source: SciCrunch Registry

http://mendel.stanford.edu/SidowLab/downloads/MAPP/

Java program that predicts the impact of all possible amino acid substitutions on the function of the protein., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: MAPP (RRID:SCR_010775) Copy   

•   Source: SciCrunch Registry

http://jbrowse.org/

A high-performance visualization tool for interactive exploration of large, integrated genomic datasets written primarily in JavaScript. It supports a wide variety of data types, including array-based and next-generation sequence data, and genomic annotations.

Proper citation: JBrowse (RRID:SCR_001004) Copy   

•   Source: SciCrunch Registry

http://zfishbook.org/

Collection of revertible protein trap gene-breaking transposon (GBT) insertional mutants in zebrafish with active or cryopreserved lines from initially identified lines. Open to community-wide contributions including expression and functional annotation and represents world-wide central hub for information on how to obtain these lines from diverse members of International Zebrafish Protein Trap Consortium (IZPTC) and integration within other zebrafish community databases including Zebrafish Information Network (ZFIN), Ensembl and National Center for Biotechnology Information. Registration allows users to save their favorite lines for easy access, request lines from Mayo Clinic catalog, contribute to line annotation with appropriate credit, and puts them on optional mailing list for future zfishbook newletters and updates.

Proper citation: zfishbook (RRID:SCR_006896) Copy   

•   Source: SciCrunch Registry

https://github.com/stephens999/ashr

Software R package for adaptive shrinkage. Implements Empirical Bayes approach for large scale hypothesis testing and false discovery rate estimation.

Proper citation: Adaptive Shrinkage in R (RRID:SCR_023486) Copy   

•   Source: SciCrunch Registry

https://github.com/rondolab/MR-PRESSO

Software R package for performing Mendelian randomization pleiotropy residual sum and outlier method.Used to identify horizontal pleiotropic outliers in multi instrument summary level MR testing.

Proper citation: MR-PRESSO (RRID:SCR_023697) Copy   

•   Source: SciCrunch Registry

https://data.broadinstitute.org/alkesgroup/Eagle/

Software package for statistical estimation of haplotype phase either within a genotyped cohort or using a phased reference panel in large scale sequencing. The package includes Eagle1 (to harness identity-by-descent among distant relatives to rapidly call phase using a fast scoring approach) and Eagle2 (to analyze a full probabilistic model similar to the diploid Li-Stephens model used by previous HMM-based methods.

Proper citation: Eagle (RRID:SCR_015991) Copy   

•   Source: SciCrunch Registry