Tools   Select Another Resource Report Type

https://biodiversityinformatics.amnh.org/open_source/dotdotgoose/

Software tool to assist with manually counting objects in images. Used for many conservation applications.

Proper citation: DotDotGoose (RRID:SCR_025485) Copy   

•   Source: SciCrunch Registry

https://github.com/dib-lab/TheGreatGenotyper

Software workflow begins by preprocessing short-read samples of raw data to create counting colored De Bruijn graph. Graph based method for population genotyping of small and structural variants. Population genotyping workflow.

Proper citation: The Great Genoytper (RRID:SCR_025487) Copy   

•   Source: SciCrunch Registry

https://shop.sartorius.com/ca/p/incucyte-ai-cell-health-analysis-software-module/BA-04871#

Software for analysis to determine live versus dead cells – no fluorescent dyes needed.

Proper citation: Incucyte Cell-By-Cell Analysis Software Module (RRID:SCR_025367) Copy   

•   Source: SciCrunch Registry

https://dokumate.com/knowledgebase/docid/

DokuMate helps standardize and reuse documents, simplifies and speeds-up editing, and automates many tedious tasks. A docId” is one of the “magic” Content Control tag names. A docId is an alphanumerical ID (e.g., “R01-01-C00”, “R01-11-100”, “R01-11-410”, “R01-30-100”) that uniquely identifies and sorts documents (e.g., Schedule C, Exhibit 1, Attachment 4.1, Appendix 1) within a larger set of documents, e.g., all documents belonging to (a) a specific RFP or (b) the set of contracts between a first party and a second party.

Proper citation: DokuMate (RRID:SCR_025402) Copy   

•   Source: SciCrunch Registry

Ratings or validation data are available for this resource

https://github.com/zhangjunpeng411/SCOM

Software application to Pan-cancer characterization of ncRNA synergistic competition. Used to predict ncRNA synergistic competition network from gene expression data and predicted ncRNA-related ceRNA networks.

Proper citation: SCOM (RRID:SCR_023738) Copy   

•   Source: SciCrunch Registry

https://gitlab.gwdg.de/MedBioinf/metabolomics/metaboserv

Browser based platform for selecting, exchanging, and visualizing metabolomics data with controlled data access. Used to facilitate collaborative metabolomics research and to enable researchers to make their experimental data findable, accessible, interoperable, and re-usable as defined by the FAIR principles.

Proper citation: MetaboSERV (RRID:SCR_025496) Copy   

•   Source: SciCrunch Registry

https://github.com/salan668/FAE

Open-source software Python package for developing and comparing radiomics models. Used to build radiomics models and evaluate them using independent testing dataset. It also provides easy model comparison and result visualization.

Proper citation: FAE (RRID:SCR_025378) Copy   

•   Source: SciCrunch Registry

http://www.okazolab.com

Software for designing and running advanced behavioral experiments and neuroscientific studies.

Proper citation: EventIDE (RRID:SCR_025412) Copy   

•   Source: SciCrunch Registry

https://nwbinspector.readthedocs.io/en/dev/

Software Python-based package designed to asses quality of Neurodata Without Borders files and based on compliance with Best Practice. Meant as companion to PyNWB validator, which checks for strict schema compliance. Attempts to apply some commonsense rules and heuristics to find data components of file that pass validation, but are probably incorrect, or suboptimal, or deviate from best practices. In other words, while PyNWB validator focuses on compliance of structure of file with the schema, the inspector focuses on compliance of actual data with best practices. Meant as data review aid. It does not catch all best practice violations, and any warnings it does produce should be checked by knowledgeable reviewer.

Proper citation: NWB Inspector (RRID:SCR_025465) Copy   

•   Source: SciCrunch Registry

https://github.com/rsquaredacademy/olsrr

Software tools for developing Ordinary Least Squares regression models.

Proper citation: olsrr (RRID:SCR_025511) Copy   

•   Source: SciCrunch Registry

https://github.com/con/duct

Software application as helper to run command, capture stdout/stderr and details about running.

Proper citation: con/duct (RRID:SCR_025436) Copy   

•   Source: SciCrunch Registry

https://github.com/sokrypton/ColabFold

Software application offers accelerated prediction of protein structures and complexes by combining homology search of MMseqs2 with AlphaFold2 or RoseTTAFold. Used for protein folding.

Proper citation: ColabFold (RRID:SCR_025453) Copy   

•   Source: SciCrunch Registry

https://github.com/google-deepmind/alphafold

Software package provides implementation of inference pipeline of AlphaFold v2. Incorporates physical and biological knowledge about protein structure, leveraging multi-sequence alignments, into design of deep learning algorithm. Used for protein structure prediction.

Proper citation: AlphaFold (RRID:SCR_025454) Copy   

•   Source: SciCrunch Registry

https://github.com/PacificBiosciences/pbmm2?tab=readme-ov-file

Software application as minimap2 frontend for PacBio native data formats. SMRT C++ wrapper for minimap2's C API.

Proper citation: pbmm2 (RRID:SCR_025549) Copy   

•   Source: SciCrunch Registry

https://github.com/franapoli/signed-ks-test

Software tool as modified R ks.test to obtain sign and force exact p-value.

Proper citation: signed ks test (RRID:SCR_025636) Copy   

•   Source: SciCrunch Registry

https://github.com/phillipnicol/scGBM

Software application for model-based dimensionality reduction of scRNA-seq data. Quantifies uncertainty in each cell's latent position and leverages these uncertainties to assess confidence associated with given cell clustering. On real and simulated single-cell data produces low-dimensional embeddings that better capture relevant biological information while removing unwanted variation. Used for model-based dimensionality reduction for single-cell RNA-seq with generalized bilinear models.

Proper citation: scGBM (RRID:SCR_025518) Copy   

•   Source: SciCrunch Registry

https://github.com/lab-medvedeva/GADES-main

Software package to compute distance matrices in sparse or dense mode with GPU or CPU.

Proper citation: GPU-assisted Distance Estimation Software (RRID:SCR_025519) Copy   

•   Source: SciCrunch Registry

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

Software R package for identifying mutational signatures of single nucleotide variants (SNVs) from high-throughput experiments.

Proper citation: SomaticSignatures (RRID:SCR_025620) Copy   

•   Source: SciCrunch Registry

https://academic.oup.com/biostatistics/article/23/4/1200/6561796

Software for multi-omic data integration. Used to jointly decompose multiple biologically related experimental data sets with biological and technological relationships that can be structured into the decomposition.

Proper citation: 2s-LCA (RRID:SCR_025613) Copy   

•   Source: SciCrunch Registry

https://academic.oup.com/bioinformatics/article/35/12/2159/5184284

Algorithm for regulatory network inference using gradient boosting, based on GENIE3 architecture. Used for inference of gene regulatory networks.

Proper citation: GRNBoost2 (RRID:SCR_025614) Copy   

•   Source: SciCrunch Registry