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https://github.com/BodenmillerGroup/imctools

Software Python package that implements preprocessing pipeline for imaging mass cytometry data. Can convert IMC raw files to tiff files that are used as inputs into CellProfiller, Ilastik, Fiji etc.

Proper citation: imctools (RRID:SCR_017132) Copy   

•   Source: SciCrunch Registry

https://github.com/colinvaz/nmf-toolbox

Software toolbox for performing Non-negative Matrix Factorization (NMF) and several variants. Used to factorize one non negative matrix into two non negative factors, that is basis matrix and coefficient matrix. Applied in bioinformatics as data mining approach.

Proper citation: NMF Toolbox (RRID:SCR_017069) Copy   

•   Source: SciCrunch Registry

https://github.com/AlexsLemonade/refinebio

Software tool to uniformly process and normalize large amounts of data. Harmonizes petabytes of publicly available biological data into ready-to-use datasets for cancer researchers and AI/ML scientists.

Proper citation: refine.bio (RRID:SCR_017471) Copy   

•   Source: SciCrunch Registry

http://www.biosoft.com/w/assayzap.htm

Software tool as universal assay calculator for RIA, ELISA, IRMA, colorimetric or any other type of assay by Biosoft. Maintains record for each assay, and enables standard curve and QCs to be compared and adjusted. Can process data from 96 and 384-well plate readers in any order.

Proper citation: AssayZap (RRID:SCR_016991) Copy   

•   Source: SciCrunch Registry

http://hmri.info

Software toolbox for quantitative MRI in neuroscience and clinical research. Open source and flexible tool for qMRI data handling and processing. Allows estimation of high quality multi parameter qMRI maps followed by spatial registration in common space for statistical analysis.

Proper citation: hMRI-toolbox (RRID:SCR_017682) Copy   

•   Source: SciCrunch Registry

https://github.com/hemberg-lab/scmap

Software tool for unsupervised projection of single cell RNA-seq data. Used for projecting cells from scRNA-seq data set onto cell types or individual cells from other experiments.

Proper citation: Scmap (RRID:SCR_017338) Copy   

•   Source: SciCrunch Registry

https://github.com/taborlab/FlowCal

Open source software tool for automatically converting flow cytometry data from arbitrary to calibrated units. Can be run using intuitive Microsoft Excel interface, or customizable Python scripts. Software accepts Flow Cytometry Standard (FCS) files as inputs and is compatible with different calibration particles, fluorescent probes, and cell types. Automatically gates data, calculates common statistics, and produces plots.

Proper citation: FlowCal (RRID:SCR_018140) Copy   

•   Source: SciCrunch Registry

https://github.com/Nevermore520/NeuronTools

Software tools for converting data files into persistence diagrams and distance matrices.

Proper citation: Neuron Tools (RRID:SCR_017450) Copy   

•   Source: SciCrunch Registry

https://github.com/wdecoster/nanofilt

Software tool written in Python to perform its filtering based on mean read quality and GC content and read length. Used for filtering and trimming of long read sequencing data.

Proper citation: NanoFilt (RRID:SCR_016966) Copy   

•   Source: SciCrunch Registry

https://github.com/mandricigor/ScaffMatch

Software tool as scaffolding algorithm based on maximum weight matching able to produce high quality scaffolds from next generation sequencing data (reads and contigs). Able to handle reads with both short and long insert sizes.

Proper citation: ScaffMatch (RRID:SCR_017025) Copy   

•   Source: SciCrunch Registry

https://bitbucket.org/nicofmay/basta-bayesian-structured-coalescent-approximation/src/master/

Software package as Bayesian method to infer migration from genetic data. Implemented in BEAST2 that combines accuracy of methods based on structured coalescent with computational efficiency required to handle more than few populations.

Proper citation: BASTA (RRID:SCR_017303) Copy   

•   Source: SciCrunch Registry

https://github.com/berenslab/EphysExtraction

Software tool as code to extract electrophysiological parameters of neurons. Code is continuously being updated to handle more kinds of voltage traces and extract different kinds of features.

Proper citation: EphysExtraction (RRID:SCR_018193) Copy   

•   Source: SciCrunch Registry

https://github.com/lufuhao/GeneSyntenyPipeline

Software pipeline was designed to draw gene synteny plot between genomes and obtain 1 to 1 gene pairs from each genome.

Proper citation: GeneSyntenyPipeline (RRID:SCR_018198) Copy   

•   Source: SciCrunch Registry

https://geomagic-studio.software.informer.com/12.0/

Software tool to convert 3D scans into parametric models. Transforms 3D scan data into highly accurate surface, polygon and native CAD models. Used for reverse engineering, product design, rapid prototyping and analysis.

Proper citation: GEOMAGIC Studio (RRID:SCR_016978) Copy   

•   Source: SciCrunch Registry

https://nidagenetics.org/

Site for collection and distribution of clinical data related to genetic analysis of drug abuse phenotypes. Anonymous data on family structure, age, sex, clinical status, and diagnosis, DNA samples and cell line cultures, and data derived from genotyping and other genetic analyses of these clinical data and biomaterials, are distributed to qualified researchers studying genetics of mental disorders and other complex diseases at recognized biomedical research facilities. Phenotypic and Genetic data will be made available to general public on release dates through distribution mechanisms specified on website.

Proper citation: National Institute on Drug Abuse Center for Genetic Studies (RRID:SCR_013061) Copy   

•   Source: SciCrunch Registry

https://www.niaid.nih.gov/diseases-conditions/coronaviruses

Information about coronaviruses, including COVID-19. NIAID provides research funding and resources for scientific community to facilitate development of vaccines, therapeutics, and diagnostics for infectious diseases, including those caused by coronaviruses.

Proper citation: NIAID Overview of Coronaviruses (RRID:SCR_018290) Copy   

•   Source: SciCrunch Registry

https://github.com/nservant/HiC-Pro

Software tool as optimized and flexible pipeline for Hi-C data processing. Used to process Hi-C data, from raw fastq files, paired end Illumina data, to normalized contact maps.

Proper citation: HiC-Pro (RRID:SCR_017643) Copy   

•   Source: SciCrunch Registry

https://github.com/sansomlab/tenx

Pipeline for the analysis of 10x single cell RNA sequencing data. Collection of python3 pipelines and Rscripts to analyze data generated with the 10x Genomics platform. The pipelines are based on 10x's Cell Ranger pipeline for mapping and quantitation and the R Seurat package for downstream analysis.

Proper citation: tenx (RRID:SCR_016957) Copy   

•   Source: SciCrunch Registry

https://github.com/NOCIONS/letswave6/wiki/Download-and-setup

Open source electroencephalogram (EEG) signal processing toolbox to process and visualise EEG/MEG data and other neurophysiological signals.

Proper citation: Letswave (RRID:SCR_016414) Copy   

•   Source: SciCrunch Registry

https://www.fil.ion.ucl.ac.uk/spm/ext/#TSDiffAna

Software tool developed for Statistical Parametric Mapping (SPM) that computes slicewise scan by scan difference and standard deviations. Used to examine quality of image timeseries.

Proper citation: TSDiffAna (RRID:SCR_016656) Copy   

•   Source: SciCrunch Registry