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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
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
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
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
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
https://community.brain-map.org/t/allen-human-reference-atlas-3d-2020-new/405
Parcellation of adult human brain in 3D, labeling every voxel with brain structure spanning 141 structures. These parcellations were drawn and adapted from prior 2D version of adult human brain atlas.
Proper citation: Allen Human Reference Atlas, 3D, 2020 (RRID:SCR_017764) Copy
https://github.com/isovic/racon
Software tool as de novo genome assembly from long uncorrected reads. Used to correct raw contigs generated by rapid assembly methods which do not include consensus step. Supports data produced by Pacific Biosciences and Oxford Nanopore Technologies.
Proper citation: Racon (RRID:SCR_017642) Copy
https://github.com/shendurelab/LACHESIS
Software tool for chromosome scale scaffolding of de novo genome assemblies based on chromatin interactions.Method exploits signal of genomic proximity in Hi-C datasets for ultra long range scaffolding of de novo genome assemblies.
Proper citation: LACHESIS (RRID:SCR_017644) Copy
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
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
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
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
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
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
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
Open platform for analyzing and sharing neuroimaging data from human brain imaging research studies. Brain Imaging Data Structure ( BIDS) compliant database. Formerly known as OpenfMRI. Data archives to hold magnetic resonance imaging data. Platform for sharing MRI, MEG, EEG, iEEG, and ECoG data.
Proper citation: OpenNeuro (RRID:SCR_005031) Copy
Ratings or validation data are available for this resource
Portal to interactively visualize genomic data. Provides reference sequences and working draft assemblies for collection of genomes and access to ENCODE and Neanderthal projects. Includes collection of vertebrate and model organism assemblies and annotations, along with suite of tools for viewing, analyzing and downloading data.
Proper citation: UCSC Genome Browser (RRID:SCR_005780) Copy
https://www.ncbi.nlm.nih.gov/geo/
Functional genomics data repository supporting MIAME-compliant data submissions. Includes microarray-based experiments measuring the abundance of mRNA, genomic DNA, and protein molecules, as well as non-array-based technologies such as serial analysis of gene expression (SAGE) and mass spectrometry proteomic technology. Array- and sequence-based data are accepted. Collection of curated gene expression DataSets, as well as original Series and Platform records. The database can be searched using keywords, organism, DataSet type and authors. DataSet records contain additional resources including cluster tools and differential expression queries.
Proper citation: Gene Expression Omnibus (GEO) (RRID:SCR_005012) Copy
Issue
Software package for analysis of brain imaging data sequences. Sequences can be a series of images from different cohorts, or time-series from same subject. Current release is designed for analysis of fMRI, PET, SPECT, EEG and MEG.
Proper citation: SPM (RRID:SCR_007037) Copy
Seattle based independent, nonprofit medical research organization dedicated to accelerating the understanding of how human brain works. Provides free data and tools to researchers and educators and variety of unique online public resources for exploring the nervous system. Integrates gene expression data and neuroanatomy, along with data search and viewing tools, these resources are openly accessible via the Allen Brain Atlas data portal. Provides Allen Mouse Brain, Allen Spinal Cord Atlas, Allen Developing Mouse Brain Atlas, Allen Human Brain Atlas,Allen Mouse Brain Connectivity Atlas, Allen Cell Type Database, The Ivy Glioblastoma Atlas Project (Ivy GAP), The BrainSpan Atlas of the Developing Human Brain.
Proper citation: Allen Institute for Brain Science (RRID:SCR_006491) Copy
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