Tools   Select Another Resource Report Type

https://github.com/zhoujt1994/scHiCluster

Software Python package for single-cell chromosome contact data analysis. It includes the identification of cell types (clusters), loop calling in cell types, and domain and compartment calling in single cells. Facilitates visualization and comparison of single-cell 3D genomes.

Proper citation: scHiCluster (RRID:SCR_027854) Copy   

•   Source: SciCrunch Registry

https://opensourcephysics.github.io/tracker-website/

Software video analysis and modeling tool developed within the Open Source Physics (OSP) Java framework. Allows frame-by-frame tracking of anatomical landmarks and articulated structures from video recordings, enabling the extraction of time-dependent kinematic variables such as displacement, velocity, and acceleration. Tracker is well suited for biomechanical analyses of articulated systems, as it supports joint-based rotations, reference-frame definition, and the export of quantitative motion data for further post-processing.

Proper citation: Tracker (RRID:SCR_027845) Copy   

•   Source: SciCrunch Registry

https://coast.noaa.gov/digitalcoast/tools/btm.html

Software set of tools useful in the analysis of benthic terrain. Includes tools for geomorphology and classification.

Proper citation: Benthic Terrain Modeler (RRID:SCR_027926) Copy   

•   Source: SciCrunch Registry

https://github.com/NOW-Lab/STICR

Code to conduct combinatorial barcoding. scRNA-seq-compatible tracer for identifying clonal relationships.

Proper citation: STICR (RRID:SCR_027856) Copy   

•   Source: SciCrunch Registry

https://github.com/blaserlab/blaseRtools/tree/v0.0.0.9202

Software R tools for Blaser Lab Data Analysis. Package includes commonly used functions for R analysis in the Blaser Lab.

Proper citation: blaseRtools (RRID:SCR_027871) Copy   

•   Source: SciCrunch Registry

https://sourceforge.net/projects/sivic/

Software framework and application suite for processing and visualization of DICOM MR Spectroscopy data. Through the use of DICOM, SIVIC aims to facilitate the application of MRS in medical imaging studies.

Proper citation: Spectroscopic Imaging, VIsualization, and Computing (SIVIC) (RRID:SCR_027875) Copy   

•   Source: SciCrunch Registry

https://pypi.org/project/llm-pathway-curator/

Software quality-assurance layer for pathway enrichment interpretation that converts enrichment term lists into context-conditioned, evidence-linked, schema-bounded claims and assigns PASS/ABSTAIN/FAIL via predefined, rule-based audit gates (stability, context validity stress tests, evidence-link integrity, and contradiction checks), producing decision-grade reports with audit logs. The LLM is confined to proposal-only steps; final decisions are mechanical and reproducible.

Proper citation: LLM-PathwayCurator (RRID:SCR_027964) Copy   

•   Source: SciCrunch Registry

https://bio.tools/dupradar

Software R package for assessment of PCR artifacts in RNA-Seq data. Used for duplication rate quality control for RNA-Seq datasets.

Proper citation: dupRadar (RRID:SCR_027976) Copy   

•   Source: SciCrunch Registry

https://github.com/AlexanRNA/nanowgs/releases/tag/v0.0.2

Nextflow pipeline to process whole genome long-read sequencing data generated in the context of ASAP project.

Proper citation: NanoWGS (RRID:SCR_028113) Copy   

•   Source: SciCrunch Registry

https://ipfx.readthedocs.io/

Software Python package for computing intrinsic cell features from electrophysiology data. Used to compute intrinsic cell features from intracellular electrophysiology data.

Proper citation: Intrinsic Physiology Feature Extractor (RRID:SCR_028075) Copy   

•   Source: SciCrunch Registry

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

Software R package for reference sequence checksums for provenance identification in RNA-seq. Performs numerous annotation and metadata gathering tasks on behalf of users during the import of transcript counts and abundance from quantification tools such as salmon. Data are imported as SummarizedExperiment objects with associated GenomicRanges metadata. Correct metadata is added automatically via reference sequence digests, facilitating genomic analyses and assisting in computational reproducibility.

Proper citation: tximeta (RRID:SCR_028005) Copy   

•   Source: SciCrunch Registry

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

Software application for de novo identification and extraction of differentially methylated regions (DMRs) from the human genome using Whole Genome Bisulfite Sequencing (WGBS) and Illumina Infinium Array (450K and EPIC) data. Provides functionality for filtering probes possibly confounded by SNPs and cross-hybridisation. Includes GRanges generation and plotting functions.

Proper citation: DMRcate (RRID:SCR_028007) Copy   

•   Source: SciCrunch Registry

https://jokergoo.github.io/rGREAT/

Software R package for functional enrichment on genomic regions. Functional enrichment analysis directly performed on genomic regions.

Proper citation: rGREAT (RRID:SCR_028008) Copy   

•   Source: SciCrunch Registry

https://histoatlas.com

Pan-cancer morphology atlas linking histological features to molecular and clinical outcomes. Structured way to explore cancer morphology at scale and connect tissue organization with patient outcomes and molecular signatures, enabling translational researchers to systematically discover and evaluate pathology-based biomarkers.

Proper citation: HistoAtlas (RRID:SCR_028056) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/compareGroups/

Software R package to create tables displaying results of univariate analyses, stratified or not by categorical variable groupings.

Proper citation: compareGroups (RRID:SCR_027994) Copy   

•   Source: SciCrunch Registry

https://github.com/capuccino26/POLY_PIPELINE

Software data analysis pipeline for spatial transcriptomics data tailored to polyploid organisms.

Proper citation: Poly Pipeline (RRID:SCR_027993) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/regioneR

Software R package to work with genomic regions. In addition to predefined randomization and evaluation strategies, regioneR is fully customizable. Implements function to evaluate local specificity of detected association. Used for association analysis of genomic regions based on permutation tests.

Proper citation: regioneR (RRID:SCR_028251) Copy   

•   Source: SciCrunch Registry

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

Software package that allows simultaneous analysis of associations between genomic region sets, enabling clustering of data and creation of graphs. Incorporates strategy to improve p-value calculations and normalize z-scores coming from multiple analysis to allow for their direct comparison. Builds upon regioneR by adding new plotting functions for obtaining publication-ready graphs.

Proper citation: regioneReloaded (RRID:SCR_028252) Copy   

•   Source: SciCrunch Registry

https://github.com/ZhuoliHuang/CIMA_BMI_paper

Source analysis and data processing code for article titled "Single-Cell Multi-Omics Insights into BMI-Mediated Immune-Related Disease Risk".

Proper citation: CIMA_BMI_paper (RRID:SCR_028241) Copy   

•   Source: SciCrunch Registry

https://github.com/brentp/somalier

Software application for rapid relatedness estimation for cancer and germline studies using efficient genome sketches extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF. Used for rapid relatedness estimation for cancer and germline studies using efficient genome sketches.

Proper citation: somalier (RRID:SCR_028167) Copy   

•   Source: SciCrunch Registry