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https://github.com/zhengkaiyu/FIMAS
Software tool to perform basic and specific analysis procedures on fluorescent microscopy and fluorescent lifetime imaging microscopy data. Requires MATLAB with image processing and statistical toolboxes. Can import fluorescent data from Olympus, Biorad, Femtonics, TIFF, Excel, ASCII files.
Proper citation: Fluorescent Imaging Analysis Software FIMAS (RRID:SCR_018311) Copy
https://www.sanger.ac.uk/science/tools/reapr
Software tool to identify errors in genome assemblies without need for reference sequence. Can be used in any stage of assembly pipeline to automatically break incorrect scaffolds and flag other errors in assembly for manual inspection. Reports mis-assemblies and other warnings, and produces new broken assembly based on error calls.
Proper citation: Recognition of Errors in Assemblies using Paired Reads (RRID:SCR_017625) Copy
http://tools.thermofisher.com/content/sfs/manuals/cms_040970.pdf
Automated PCR instrument for automated amplification of nucleic acids with Polymerase Chain Reaction. It has reaction volumes of up to 50 uL and sample temperature range of 4 to 99.9 C.
Proper citation: Thermo Fisher: Applied Biosystems: GeneAmp 9700 PCR Thermocycler System (RRID:SCR_018436) Copy
Provides services for USED lab instrument repairs.Recertified laboratory equipment commercially available. Comes fully re-certified to manufacturers standards with 90 day warranty.
Proper citation: Certified Genetool, Inc. (RRID:SCR_018678) Copy
All Dimensions publications, datasets, and clinical trials related to COVID-19, updated daily.
Proper citation: Dimensions COVID-19 publications, datasets and clinical trials (RRID:SCR_018276) Copy
Open community of researchers, educators, and professionals with goal of improving way we develop, share, use, and re-use agent based and computational models for study of social and ecological systems. Develops and maintains CoMSES Model Library, digital repository that supports discovery and good practices for software citation, digital preservation, reproducibility, and reuse.
Proper citation: CoMSES Net (RRID:SCR_017598) Copy
Library with storage capacity of over million compounds possessing diversified structures. Coupled with this library will be advanced sample handling, information management and quality control systems. As important material and information resource, CNCL will work with both domestic and international stakeholders to promote sustained development of Chinese pharmaceutical industry.
Proper citation: Chinese National Compound Library (RRID:SCR_018723) Copy
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
https://openwetware.org/wiki/HughesLab:JTK_Cycle
Software R package for Detecting Rhythmic Components in Genome-Scale Data Sets. Non-parametric algorithm to identify rhythmic components in large datasets. Identifies and characterizes cycling variables in large datasets.
Proper citation: JTK_CYCLE (RRID:SCR_017962) Copy
https://www.med.upenn.edu/cbica/captk/
Software platform for analysis of radiographic cancer images. Used as quantitative imaging analytics for precision diagnostics and predictive modeling of clinical outcome.
Proper citation: Cancer Imaging Phenomics Toolkit (RRID:SCR_017323) Copy
Open Source software package for digital pathology image analysis. Used for whole slide image analysis and digital pathology. Provides researchers with batch processing and scripting functionality, and extensible platform with which to develop and share new algorithms to analyze complex tissue images.
Proper citation: QuPath (RRID:SCR_018257) Copy
https://github.com/nebneuron/neural-ideal
Software package for extracting neural activity codes.
Proper citation: Neural Ideal (RRID:SCR_017448) Copy
https://github.com/flatironinstitute/mountainsort
Neurophysiological spike sorting software.
Proper citation: MountainSort (RRID:SCR_017446) Copy
Open knowledge base that can be read and edited by both humans and machines. Storage for structured data of its Wikimedia sister projects including Wikipedia, Wikivoyage, Wiktionary, Wikisource, and others. Provides support to many other sites and services beyond just Wikimedia projects.
Proper citation: Wikidata (RRID:SCR_018492) 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
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
https://chlorobox.mpimp-golm.mpg.de/geseq.html
Software tool for rapid and accurate annotation of organelle genomes, in particular chloroplast genomes.
Proper citation: GeSeq (RRID:SCR_017336) 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://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://www.mbfbioscience.com/stereo-investigator-cleared-tissue-edition
Software tool for unbiased stereology to be used on cleared tissue. Used to analyze intact, cleared tissue specimens imaged with light sheet or confocal microscopes. Includes number, length, area and volume analyses.
Proper citation: Stereo Investigator - Cleared Tissue Edition (RRID:SCR_017668) Copy
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