Tools   Select Another Resource Report Type

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://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/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://rubygems.org/gems/viral_seq

Ruby Gem with bioinformatics tools for processing viral NGS data. Specifically for Primer-ID sequencing and HIV drug resistance analysis.

Proper citation: viral_seq (RRID:SCR_018515) 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://github.com/ttrogers/DecodingDynamic

Data, code, and notebooks for replicating analyses reported in Rogers et al., Evidence for deep, distributed and dynamic semantic code in human ventral anterior temporal cortex.

Proper citation: DecodingDynamic (RRID:SCR_021099) Copy   

•   Source: SciCrunch Registry

http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/genomic_curated_CDF.asp

Brainarray custom CDFs for processing raw Affymetrix data. Used to map probe to probesets. Oligonucleotide probes on GeneChips are reorganized based on latest genome and transcriptome information.

Proper citation: CustomCDF (RRID:SCR_018527) Copy   

•   Source: SciCrunch Registry

https://hdmf.readthedocs.io/

Open source software Python package for working with hierarchical data. Provides APIs for specifying data models, reading and writing data to different storage backends, and representing data with Python object.Used for working with standardizing, reading, and writing hierarchical object data.

Proper citation: Hierarchical Data Modeling Framework (RRID:SCR_021303) Copy   

•   Source: SciCrunch Registry

http://www.msbioworks.com/

A protein mass spectrometry service provider that delivers data to industrial and government organizations as well as academic institutions. Protein services include protein identification, mapping, profiling, and mass measurement. Post-translational modification services include PTM profiling, phospho-screening, and glyco-screening. Quantitative proteomics services include workflows for label free, TMT, SILAC, and PRM. MS Bioworks also provides immunoprecipitated protein analysis and custom analysis.

Proper citation: MS Bioworks (RRID:SCR_001043) 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://kidsfirstdrc.org/portal/portal-features/

Portal for analysis and interpretation of pediatric genomic and clinical data to advance personalized medicine for detection, therapy, and management of childhood cancer and structural birth defects. For patients, researchers, and clinicians to create centralized database of well curated clinical and genetic sequence data from patients with childhood cancer or structural birth defects.

Proper citation: Kids First Data Resource Portal (RRID:SCR_016493) Copy   

•   Source: SciCrunch Registry

https://satijalab.org/seurat/get_started.html

Software as R package designed for QC, analysis, and exploration of single cell RNA-seq data. Enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data.

Proper citation: Seurat (RRID:SCR_016341) 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/davidaknowles/leafcutter/

Software tool for identifying and quantifying RNA splicing variation. Used to study sample and population variation in intron splicing. Identifies variable intron splicing events from short read RNA-seq data and finds alternative splicing events of high complexity. Used for detecting differential splicing between sample groups, and for mapping splicing quantitative trait loci (sQTLs).

Proper citation: LeafCutter (RRID:SCR_017639) 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://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

http://www.nitrc.org/projects/nutil/

Software toolbox to simplify and streamline mechanism of pre and post processing 2D brain image data. Neuroscience image processing and analysis utilities. Stand alone application that runs on all operating systems.

Proper citation: Nutil - Neuroimaging utilities (RRID:SCR_017183) Copy   

•   Source: SciCrunch Registry