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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

https://github.com/TheLeeLab/cameraCalibrationCMOS

Software for performing pixelwise calibration of sCMOS cameras. MATLAB code and instructions for routine camera calibration.

Proper citation: cameraCalibrationCMOS (RRID:SCR_025339) Copy   

•   Source: SciCrunch Registry

https://github.com/marbl/Winnowmap

Software tool as long-read mapping algorithm optimized for mapping ONT and PacBio reads to repetitive reference sequences. Winnowmap2 computes each read mapping through collection of confident subalignments. This approach is more tolerant of structural variation and more sensitive to paralog-specific variants within repeats.

Proper citation: Winnowmap (RRID:SCR_025349) Copy   

•   Source: SciCrunch Registry

https://readysetpotato.com/

Software tool that helps users write experimental protocols.

Proper citation: Ready Set Potato (RRID:SCR_025289) Copy   

•   Source: SciCrunch Registry

https://search.kg.ebrains.eu/?category=Project#904b7981-0c68-4af6-b3bb-3d9a648b3a7c

Continuous 3D reference atlas for postnatal mouse brain.

Proper citation: Developmental Mouse Brain atlas (RRID:SCR_025324) Copy   

•   Source: SciCrunch Registry

https://www.yworks.com/products/yed

Software desktop application as general purpose diagramming program with multi-document interface. Cross-platform Java application to generate high-quality diagrams. Runs on Windows, Linux, Mac OS, and other platforms that support Java Virtual Machine.

Proper citation: yEd (RRID:SCR_025325) Copy   

•   Source: SciCrunch Registry

https://www.thermofisher.com/us/en/home/industrial/spectroscopy-elemental-isotope-analysis/molecular-spectroscopy/uv-vis-spectrophotometry/instruments/nanodrop/software.html

Operating software for Thermo Scientific NanoDrop 1000 Spectrophotometer. Free NanoDrop operating software to update your instrument.

Proper citation: Thermo Scientific NanoDrop 1000 Software (RRID:SCR_025282) Copy   

•   Source: SciCrunch Registry

https://whatshap.readthedocs.io/en/latest/

Software for phasing genomic variants using DNA sequencing reads, also called read-based phasing or haplotype assembly. Used for long reads, but works also well with short reads.

Proper citation: WhatsHap (RRID:SCR_025319) Copy   

•   Source: SciCrunch Registry

https://www.bruker.com/en/products-and-solutions/preclinical-imaging/paravision-360.html

Software for preclinical imaging integrated with Bruker MRI spectrometers. Used with Bruker MRI, PET/MR, and PET/CT instruments. Enables easy and high throughput imaging. All images, protocols, and subjects are in one location with inherent co-registration, image fusion, data processing, and analysis.

Proper citation: ParaVision 360 (RRID:SCR_025295) Copy   

•   Source: SciCrunch Registry

https://github.com/COMBINE-lab/maximum-likelihood-relatedness-estimation

C++ program to infer biological relatedness from low coverage 2nd generation sequencing data. It uses information from genotype likelihoods rather than observed genotypes in maximum likelihood framework in order to estimate the overall coefficient of relatedness as well as individual kinship components between two samples. Maximum Likelihood Estimation of Biological Relatedness from Low Coverage Sequencing Data.

Proper citation: lcMLkin (RRID:SCR_025418) Copy   

•   Source: SciCrunch Registry

https://pvactools.readthedocs.io/en/latest/

Software toolkit to identify and visualize cancer neoantigens. Cancer immunotherapy tools suite consisting of following tools: pVACseq as cancer immunotherapy pipeline for identifying and prioritizing neoantigens from VCF file; pVACbind as cancer immunotherapy pipeline for identifying and prioritizing neoantigens from FASTA file; pVACfuse as tool for detecting neoantigens resulting from gene fusions; pVACvector as tool designed to aid specifically in construction of DNA-based cancer vaccines; pVACview as application based on R Shiny that assists users in reviewing, exploring and prioritizing neoantigens from results of pVACtools processes for personalized cancer vaccine design.

Proper citation: pVACtools (RRID:SCR_025435) Copy   

•   Source: SciCrunch Registry

https://github.com/monologue0924/COMSOL-model-of-Magnetic-coil-

Software application as model of magnetic field distribution of magnetic coil visualized using COMSOL Multiphysics.

Proper citation: COMSOL model of Magnetic coil (RRID:SCR_025426) Copy   

•   Source: SciCrunch Registry

https://github.com/gui11aume/starcode

Software for DNA sequence clustering. General purpose DNA sequence clustering tool with strong focus on error correction.

Proper citation: Starcode (RRID:SCR_025483) Copy   

•   Source: SciCrunch Registry

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://CRAN.R-project.org/package=aod

Software R package to analyse overdispersed counts or proportions.

Proper citation: aod: Analysis of Overdispersed Data (RRID:SCR_025516) 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

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://www.lyrasis.org

Organization that works with knowledge professionals to create, support and deliver programs, services and technologies that allow for equitable access to world knowledge and cultural heritage. Hosts data-migration, content licensing, and community supported soft​ware programs for libraries, archives, museums and research organizations worldwide.​​​

Proper citation: Lyrasis (RRID:SCR_025403) 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

http://www.fieldgenetics.com/pages/aboutCervus_Overview.jsp

Software package for parentage analysis in plant and animal populations. It combines robust likelihood-based method with simple graphical interface.

Proper citation: CERVUS (RRID:SCR_025446) Copy   

•   Source: SciCrunch Registry