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https://github.com/instadeepai/nucleotide-transformer

Genomic language model trained on cross species data.

Proper citation: Nucleotide Transformer (RRID:SCR_027472) Copy   

•   Source: SciCrunch Registry

https://gpspalm.biocuckoo.cn/

Software deep learning-based graphic presentation system for the prediction of S-palmitoylation sites in proteins.

Proper citation: GPS-Palm (RRID:SCR_027506) Copy   

•   Source: SciCrunch Registry

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

Object-oriented software for model-robust covariance matrix estimators. Starting out from the basic robust Eicker-Huber-White sandwich covariance methods include: heteroscedasticity-consistent (HC) covariances for cross-section data; heteroscedasticity- and autocorrelation-consistent (HAC) covariances for time series data (such as Andrews' kernel HAC, Newey-West, and WEAVE estimators); clustered covariances (one-way and multi-way); panel and panel-corrected covariances; outer-product-of-gradients covariances; and (clustered) bootstrap covariances. All methods are applicable to (generalized) linear model objects fitted by lm() and glm() but can also be adapted to other classes through S3 methods.

Proper citation: sandwich (RRID:SCR_027691) Copy   

•   Source: SciCrunch Registry

https://github.com/ncc-gap/GCATWorkflow

Software cancer genome and RNA sequencing data analysis pipeline that detects genomic variants and transcriptomic changes.

Proper citation: GCAT Workflow (RRID:SCR_027692) Copy   

•   Source: SciCrunch Registry

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

Software package for the R Environment. Used for estimating multidimensional item response theory parameters for exploratory and confirmatory models by using maximum-likelihood meth- ods.

Proper citation: mirt (RRID:SCR_027662) Copy   

•   Source: SciCrunch Registry

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

Software R package uses inverse probability weighting methods to estimate treatment effect under marginal structure model for the cause-specific hazard of competing risk events. Estimates also the cumulative incidence function (i.e. risk) of the potential outcomes, and provides inference on risk difference and risk ratio.

Proper citation: cmprskcoxmsm (RRID:SCR_027665) Copy   

•   Source: SciCrunch Registry

https://gitlab.com/uniluxembourg/lcsb/systems-ecology/pathofact2

Software integrative pipeline for antimicrobial resistance genes, virulence factors, toxins, and biosynthetic gene clusters prediction in metagenomes. Used for predicting microbiome-based pathogenicity and resistance to better understand and address challenges posed by antimicrobial resistance and infectious diseases.

Proper citation: PathoFact2 (RRID:SCR_027650) Copy   

•   Source: SciCrunch Registry

https://www.github.com/bactopia/bactopia

Software pipeline for complete analysis of bacterial genomes.

Proper citation: Bactopia (RRID:SCR_027581) Copy   

•   Source: SciCrunch Registry

https://github.com/INCF/swc-specification

Software repository contains files needed to build the standard and its supplementary documentation. Changes are automatically pushed and built. Information about the SWC file specification.

Proper citation: SWC format (RRID:SCR_027631) Copy   

•   Source: SciCrunch Registry

https://novosparc.readthedocs.io/

Software package for flexible spatial reconstruction of single-cell gene expression with optimal transport. Framework for de novo spatial reconstruction of single-cell gene expression. Assigns cells to tissue locations using probabilistic/optimal-transport models, with or without prior marker information, and returns spatial maps and assignment probabilities.

Proper citation: novoSpaRc (RRID:SCR_027635) Copy   

•   Source: SciCrunch Registry

https://alleninstitute.github.io/CCF-MAP/docs/HOMBA_ontology_v1.html

Harmonized cross-species taxonomy of brain and spinal cord structures. Derived from the Allen Developing Human Brain Atlas (DHBA) ontology, the HOMBA is hierarchical, allowing users to aggregate structures from fine grain parcellations to broad regions. Terminology is harmonized across human, primate, and rodent structures with synonymous terms and includes transient developmental structures. HOMBA is designed for neuroanatomical applications including brain sampling and dissection, tissue block mapping, atlas building, cell-type and pathology localization, and linking cross-species and developmental datasets.

Proper citation: Harmonized Ontology of Mammalian Brain Anatomy (HOMBA) (RRID:SCR_027628) Copy   

•   Source: SciCrunch Registry

https://stardist.net/

Software application for object detection with Star-convex Shapes. Used for phase-contrast cell images.

Proper citation: StarDist (RRID:SCR_027715) Copy   

•   Source: SciCrunch Registry

https://bitbucket.org/bbglab/oncodriveclustl/src/master

Software application to detect significant clustering signals across genomic regions. Sequence-based clustering method to identify cancer drivers.

Proper citation: OncodriveCLUSTL (RRID:SCR_027730) Copy   

•   Source: SciCrunch Registry

https://bitbucket.org/bbglab/oncodrivefml/src/master

Software tool that estimates accumulated functional impact bias of somatic mutations in any genomic region of interest based on local simulation of the mutational process affecting it.

Proper citation: OncodriveFML (RRID:SCR_027731) Copy   

•   Source: SciCrunch Registry

https://github.com/instadeepai/instanovo

Source code for training and inference of InstaNovo and InstaNovo+. InstaNovo is a transformer neural network with the ability to translate fragment ion peaks into the sequence of amino acids that make up the studied peptide(s).

Proper citation: InstaNovo (RRID:SCR_027758) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/package=AER

Software R package contains functions, data sets, examples, demos, and vignettes for the book Christian Kleiber and Achim Zeileis (2008), Applied Econometrics with R, Springer-Verlag, New York. ISBN 978-0-387-77316-2.

Proper citation: AER: Applied Econometrics with R (RRID:SCR_027778) Copy   

•   Source: SciCrunch Registry

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

Software R package for analysing multiple omics datasets in the context of molecular pathways, biological processes and other types of gene sets.Method that first prioritises genes through multi-omics data fusion and then identifies enriched pathways with gene-level evidence from input datasets.

Proper citation: ActivePathways (RRID:SCR_027736) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/release/data/annotation/html/BSgenome.Hsapiens.UCSC.hg38.html

Software R package containing the full genomic sequences for Homo sapiens as provided by UCSC (genome hg38, based on assembly GRCh38.p14 since 2023/01/31).

Proper citation: BSgenome Hsapiens UCSC hg38 (RRID:SCR_027738) Copy   

•   Source: SciCrunch Registry

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