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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

https://github.com/nanoporetech/pod5-file-format

File format for storing nanopore DNA data in an easily accessible way. High performance file format for nanopore reads.

Proper citation: pod5 (RRID:SCR_028166) Copy   

•   Source: SciCrunch Registry

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

Software R package provides some legacy utility functions for performing single-cell analyses. Most of these functions are deprecated in favor of newer, more performant alternatives. We just keep this package around for back-compatibility and to point to the replacement functions.

Proper citation: scuttle (RRID:SCR_028419) Copy   

•   Source: SciCrunch Registry

https://www.bioconductor.org/packages/release/data/experiment/html/scRNAseq.html

Software R package for collection of public scRNA-seq datasets, provided as SingleCellExperiment objects with cell- and gene-level metadata.

Proper citation: scRNAseq (RRID:SCR_028417) Copy   

•   Source: SciCrunch Registry

https://www.bioconductor.org/packages//release/data/experiment/html/TabulaMurisData.html

Software R package for access to processed 10x (droplet) and SmartSeq2 (on FACS-sorted cells) single-cell RNA-seq data from the Tabula Muris consortium.

Proper citation: TabulaMurisData (RRID:SCR_028418) Copy   

•   Source: SciCrunch Registry

https://doi.org/10.32614/CRAN.package.pairwiseCI

Software R package provides wrapper functions to compute parametric, nonparametric, and bootstrap confidence intervals (CIs) for comparing two samples, specifically designed for all-pairs or many-to-one comparisons. It enables, but does not enforce, adjustments for multiple testing.

Proper citation: pairwiseCI (RRID:SCR_028345) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/lf_patches/

Software MATLAB toolbox for the automatic segmentation of the hippocampus in brain MRI images. It implements a novel patch-based label fusion method that cooperates with a non-rigid registration-based label fusion approach. Used to automatically and accurately segment the hippocampus in MRI scans by combining two techniques.

Proper citation: Combining a patch-based approach with a non-rigid registration-based label fusion method for the hippocampal segmentation (RRID:SCR_028349) Copy   

•   Source: SciCrunch Registry

https://mdv.ndm.ox.ac.uk/docs/documentation/using-chatmdv

Software tool as natural language interface integrated with MDV that allows users to generate high-quality interactive visualisations through natural language commands. ChatMDV employs a retrieval-augmented generation (RAG) pipeline combined with large language models (LLMs) to translate user queries into reproducible Python code and interactive output. Module to add chatbot functionality to query Multi-Dimensional Viewer projects.

Proper citation: ChatMDV (RRID:SCR_028342) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/readr/index.html

Software R package read flat files (csv, tsv, fwf) into R. Used to read rectangular data like 'csv', 'tsv', and 'fwf'. Designed to flexibly parse many types of data found in the wild, while still cleanly failing when data unexpectedly changes.

Proper citation: readr (RRID:SCR_028451) Copy   

•   Source: SciCrunch Registry

https://lume.tv/PANGEA/

Spacial neuron gene expression atlas. Interactive, server-free web application and spatial transcriptomics database designed to help researchers map and analyze gene expression within the brain. Mouse whole brain spatial transcriptomic atlas.

Proper citation: PANGEA (RRID:SCR_028559) Copy   

•   Source: SciCrunch Registry

https://www.embl-hamburg.de/biosaxs/dammif.html

Software tool for rapidly determining the low-resolution three-dimensional shape of biological macromolecules in solution using Small-Angle X-ray Scattering (SAXS) data. Used for rapid ab-initio shape determination in small-angle scattering.

Proper citation: DAMMIF (RRID:SCR_028444) Copy   

•   Source: SciCrunch Registry

https://bioconductor.posit.co/packages/3.20/data/annotation/html/IlluminaHumanMethylationEPICv2anno.20a1.hg38.html

Software R annotation package for Illumina's EPIC v2.0 methylation arrays. The version 2 covers more than 935K CpG sites in the human genome hg38. It is an update of the original EPIC v1.0 array (i.e., the 850K methylation array).

Proper citation: IlluminaHumanMethylationEPICv2anno (RRID:SCR_028569) Copy   

•   Source: SciCrunch Registry

https://gatk.broadinstitute.org/hc/en-us/articles/360036350452-VariantFiltration

Software command-line tool designed for hard-filtering variant callsets (VCF files) by applying user-defined criteria to annotate, rather than remove, low-quality variants. It marks fails in the FILTER field (e.g., using JEXL expressions to filter by DP, QD, or FS), making it essential for filtering small datasets, non-model organisms, or whenever Variant Quality Score Recalibration (VQSR) is not feasible

Proper citation: GATK VariantFiltration (RRID:SCR_028441) Copy   

•   Source: SciCrunch Registry

https://genome.ucsc.edu/goldenpath/help/bigWig.html

Command-line utility provided by the UCSC Genome Browser to convert text-based bedGraph files into indexed binary bigWig files. It is specifically used in bioinformatics to transform dense, continuous genome coverage data into a format that enables fast visualization and remote viewing in genome browsers like IGV or the UCSC Genome Browser.

Proper citation: bedGraphToBigWig (RRID:SCR_028439) Copy   

•   Source: SciCrunch Registry

https://www.scienceverse.org/metacheck/

Software R package to audit research outputs for compliance with open science best practices. Evaluates adherence to standards such as pre-registration and data availability. Used for automated checks of research outputs for best practices.

Proper citation: MetaCheck (RRID:SCR_028666) Copy   

•   Source: SciCrunch Registry

https://mycompounddiscoverer.com/

Software platform by Thermo Fisher Scientific designed for identifying, comparing, and interpreting small molecules in complex biological, environmental, and forensic samples. It uses customizable workflow, known as nodes, to automate mass spectrometry data processing, spectral library searching, and statistical analysis.Compound Discoverer is integrated with SIRIUS (via a custom workflow node) to bridge the gap between high-resolution MS/MS data and confident molecular identification. While Thermo Scientific’s Compound Discoverer excels at library searching and statistical analysis, SIRIUS provides powerful in silico tools to accurately predict molecular formulas, chemical classes, and de novo structures. High-resolution mass spectrometry (HRMS) data analysis software for untargeted metabolomics, lipidomics, and contaminant screening. Utilizes modular workflows to extract features, match spectra against libraries like mzCloud, and confidently identify complex organic compounds.

Proper citation: Compound Discoverer (RRID:SCR_028693) Copy   

•   Source: SciCrunch Registry