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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
https://github.com/lufuhao/ExonerateTransferAnnotation
Software tool as pipeline to make anntotations using cDNA and CDS sequences.
Proper citation: ExonerateTransferAnnotation (RRID:SCR_017557) Copy
https://edspace.american.edu/openbehavior/project/optimouse/
Project related to individual mice positions analysis, specifically their nose positions. Includes software tool for analysis of mouse position data designed by Hebrew University scientists. Provides open source software to analyze positions of individual mice, specifically their nose positions, in behavioral arena with the goal of minimizing error.
Proper citation: Optimouse project (RRID:SCR_021463) Copy
https://usa.jpk.com/news/2011/directoverlay-display-analysis-software-from-jpk-instruments
Software package for display of light microscopy images together with atomic force microscopy images.
Proper citation: DirectOverlay (RRID:SCR_018978) Copy
https://edspace.american.edu/openbehavior/project/mousetrap/
Project related to mouse tracking and analysis of mouse movements during computerized lab experiments. Provides open source software plugin to record and analyze mouse movements.
Proper citation: Mousetrap project (RRID:SCR_021456) Copy
https://github.com/a-h-b/dadasnake
Software tool as snakemake implementation of DADA2 to process amplicon sequencing data for microbial ecology.
Proper citation: dadasnake (RRID:SCR_019149) Copy
https://edspace.american.edu/openbehavior/project/medparse/
Project related to saving precise times of behavioral events.Provides software tool to read MedPC data into Python and Matlab.
Proper citation: MedParse project (RRID:SCR_021455) Copy
https://spikeforest.flatironinstitute.org
Software reproducible, continuously updating platform which benchmarks performance of spike sorting codes across large curated database of electrophysiological recordings with ground truth. Website and open source computing framework for evaluating and comparing spike sorting algorithms for neurophysiology data analysis. Project of Center for Computational Mathematics at Flatiron Institute.
Proper citation: SpikeForrest (RRID:SCR_019261) Copy
https://github.com/almorlio/CiLiQuant
Software tool to separate junction reads based on their linear or circular origin. Only non ambiguous junction reads are used to compare relative linear and circular transcript abundance.
Proper citation: CiLiQuant (RRID:SCR_019319) Copy
Software tool designed by Data Coordination Platform of Human Cell Atlas to process single-cell RNAseq data generated by Smart-seq2 assays.Processes stranded or unstranded, paired- or single-end, scRNA-seq data from an individual cell.
Proper citation: Smart-seq2 Single Sample Pipeline (RRID:SCR_021228) Copy
Portal as central source of Australian open government data. Used to find, explore and reuse Australia public data. Anyone can access the anonymised public data published by federal, state and local government agencies, publicly funded research data and datasets from private institutions that are in public interest.
Proper citation: Australian Government Data Portal (RRID:SCR_019159) Copy
Cloud based research platform that allows researchers and students to quickly and easily create and deploy behavioural experiments online. Online behavioral experiment builder for running behavioural studies.
Proper citation: Gorilla Experiment Builder (RRID:SCR_020991) Copy
https://edspace.american.edu/openbehavior/project/offline-behavior-video-analysis/
Project related to visualizing and quantifying movement from pre-recorded videos. Provides software toolbox for visualizing and quantifying movement.Used for summarizing animal movement data as single image ( spectral time lapse algorithm) as well as automate analysis of animal movement data.
Proper citation: Quantifying Animal Movement from Pre-recorded Videos project (RRID:SCR_021436) Copy
https://github.com/caleblareau/mgatk
Software python-based command line interface for processing .bam files with mitochondrial reads and generating high-quality heteroplasmy estimation from sequencing data. This package places a special emphasis on mitochondrial genotypes generated from single-cell genomics data, primarily mtscATAC-seq, but is generally applicable across other assays.
Proper citation: mgatk (RRID:SCR_021159) Copy
https://edspace.american.edu/openbehavior/project/boris/
Project related to computer based review of previously recorded videos or live observations. Related to study of animal and human behavior. Provides open source, multiplatform standalone program that allows user specific coding environment for computer based review of previously recorded videos or live observations.Developed by scientists from University of Turin.
Proper citation: Behavioral Observation Research Interactive Software project (RRID:SCR_021434) Copy
Open source designs for customizable, MRI compatible microdrive capable of positioning probes including stimulating electrodes, recording electrodes, drug cannulae, or optogenetic fibers within brain. Design integrates cranial implant, penetration grid for guiding probes, and microdrive body assembly with actuators. Used by neuroscience community related to electrical microstimulation, neuronal recording, and local drug delivery.
Proper citation: MRI Compatible and Customizable Microdrive Design for Neuroscience Research (RRID:SCR_019247) Copy
Software pipeline for single-nucleus RNAseq data generated by Smart-seq2 assays.Used to simultaneously process multiple libraries of single nuclei Smart-seq2 and Smart-seq4 data. For each library (nucleus), the pipeline trims paired FASTQ files, aligns trimmed reads to the genome, counts intronic and exonic reads, and calculates quality control metrics. Counts and metrics for all libraries are combined into merged Loom formatted count matrix.
Proper citation: Smart-seq2 Single Nucleus Multi Sample Pipeline (RRID:SCR_021312) Copy
https://edspace.american.edu/openbehavior/project/m-track/
Project related to tracking movement of labelled paws in grooming and freely behaving mice. Provides software toolbox for automated detection of forepaw trajectories in mice.
Proper citation: M-Track project (RRID:SCR_021433) Copy
Matchmaking platform for clinicians and scientists to facilitate collaborative research on rare and undiagnosed diseases. Used for collaborative projects that advance scientific knowledge and patient care. Currently supports Mouse, Rat, Frog, Zebrafish, Fruit Fly, Nematode Worm, Budding Yeast, Fission Yeast, and E. coli. Used to identify human ortholog of genes in these model organisms and vice versa. Scientists who register in ModelMatcher are asked to classify their genes of interest into Public or Restricted categories.The Match feature will allow Clinicians to obtain information on genes that Scientists classify as both Public and Restricted.
Proper citation: ModelMatcher (RRID:SCR_021208) Copy
https://edspace.american.edu/openbehavior/project/pathfinder/
Project to detect spatial navigation behavior in animals.Provides open source software for analyzing spatial navigation search strategies developed by University of British Columbia scientists.
Proper citation: Pathfinder project (RRID:SCR_021447) Copy
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