Tools   Select Another Resource Report Type

https://brain-bican.github.io/bkbit/

Software package contains tools to use the BICAN Knowledgebase Data Models.

Proper citation: bkbit (RRID:SCR_027564) Copy   

•   Source: SciCrunch Registry

https://lightning.ai/

Open-source software Python library that provides high-level interface for PyTorch deep learning framework.

Proper citation: PyTorch Lightning (RRID:SCR_027468) Copy   

•   Source: SciCrunch Registry

https://github.com/aertslab/create_cisTarget_databases

Code to create cisTarget databases.

Proper citation: create_cisTarget_databases (RRID:SCR_027473) Copy   

•   Source: SciCrunch Registry

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://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://alleninstitute.github.io/CCF-MAP/descriptions/marmoset_ccf.html

Three-dimensional brain reference atlas based on the RIKEN25v1 MRI-derived template, based on an average of 25 C. jacchus brains resampled to 70 um3 voxel resolution. Includes selected published subcortical parcellations to aid in comparing across parcellation schemes.

Proper citation: HOMBA Adult Marmoset Basal Ganglia Atlas (RRID:SCR_027642) 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://github.com/Core-Bioinformatics/bulkAnalyseR

Software R package for most bulk sequencing datasets. Creates shiny app for interactive data analysis and visualisation. Used for analysing and sharing bulk sequencing results.

Proper citation: bulkAnalyseR (RRID:SCR_027647) 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://satijalab.org/seurat/reference/mapquery

Convenience wrapper function around the following three functions that are often run together when mapping query data to a reference: TransferData, IntegrateEmbeddings, ProjectUMAP.

Proper citation: Seurat MapQuery (RRID:SCR_027590) 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://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://gricad-gitlab.univ-grenoble-alpes.fr/nanobubbles/pcl_detector

Software tool to detect problematic cell lines during text processing.Based on: SciSpacy NER model "en_ner_jnlpba_md" -- DNA, Cell Type, RNA, Protein, Cell Line Cellosaurus (Dump, FEV. 2021) and ICLAC (V10).

Proper citation: PCL_detector (RRID:SCR_027703) 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