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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

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

http://rsync.samba.org/

Software that provides rapid incremental file transfer.

Proper citation: rsync (RRID:SCR_003113) Copy   

•   Source: SciCrunch Registry

http://rp-www.cs.usyd.edu.au/~yangpy/software/MFGE.html

A hybrid software system for feature selection and sample classification of high-dimensional datasets. It is designed for microarray but can be applied to any other high-dimensional datasets. It uses multiple filters to produce a normalized score for each feature. The score is an indication of the usefulness of each feature. It is then translated into a frequency map with more useful features receive a higher frequency in the map.

Proper citation: MF-GE (RRID:SCR_003509) Copy   

•   Source: SciCrunch Registry

http://noble.gs.washington.edu/proj/charge/

Charge Czar is a software tool that uses a support vector machine to discriminate between +2- and +3-charged tandem mass spectra, with the goal of reducing database search time by eliminating the need to search twice with each spectrum. Charge Czar is written in Python and ANSI C. Source code for the latest version, as well as some pre-compiled versions for popular platforms (Linux, Cygwin) can be downloaded after you have agreed to the license agreement. Mass spectrometry is a particularly useful technology for the rapid and robust identification of peptides and proteins in complex mixtures. Peptide sequences can be identified by correlating their observed tandem mass spectra (MS/MS) with theoretical spectra of peptides from a sequence database. Unfortunately, to perform this search the charge of the peptide must be known, and current charge-state-determination algorithms only discriminate singly- from multiply-charged spectra: distinguishing +2 from +3, for example, is unreliable. Thus, search software is forced to search multiply-charged spectra multiple times. To minimize this inefficiency, we present a support vector machine (SVM) that quickly and reliably classifies multiply-charged spectra as having either a +2 or +3 precursor peptide ion. By classifying multiply-charged spectra, we obtain a 40% reduction in search time while maintaining an average of 99% of peptide and 99% of protein identifications originally obtained from these spectra.

Proper citation: Charge Czar: Peptide charge state determination for low-resolution tandem mass spectra (RRID:SCR_004315) Copy   

•   Source: SciCrunch Registry

http://noble.gs.washington.edu/proj/segtools/

Segtools is a Python package designed to put genomic segmentations back in the context of the genome! Using R for graphics, Segtools provides a number of modules to analyze a segmentation in various ways and help you interpret its biological relevance. Segmentations should be in BED4+ or GFF format, with the ''name'' field of each line used specifying the segment label of that line. The Segtools commands allow you to compare the properties of the segment labels with one another.

Proper citation: Segtools (RRID:SCR_004394) Copy   

•   Source: SciCrunch Registry

https://simtk.org/home/cpodes

CPODES is a numerical integrator for solving multibody dynamics problems using coordinate projection. It is based on the CVODES integrator which is part of the DOE Sundials suite. It is a multistep integrator providing variable order Adams (up to 12th order) and BDF (up to 5th order) methods for non-stiff problems and BDF (up to 5th order) for stiff problems. It uses CVODES to advance the ODE, and then performs coordinate projection back to the constraint manifold to exactly solve the DAE. The projection is also incorporated back into the error test where it permits larger steps. Binaries of this software are bundled with other SimTK Core modules.

Proper citation: CPODES numerical integrator (RRID:SCR_000766) Copy   

•   Source: SciCrunch Registry