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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
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
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
https://github.com/flatironinstitute/mountainsort
Neurophysiological spike sorting software.
Proper citation: MountainSort (RRID:SCR_017446) 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
http://www.gelifesciences.co.kr/wp-content/uploads/2016/08/IN-Cell-Developer-Toolbox-v1.9.pdf
Image analysis software for developing new cellular assay analysis routines. This software provides a selection of advanced segmentation, pre-processing and post-postprocessing tools.
Proper citation: INCell Developer Toolbox (RRID:SCR_015790) Copy
https://www.ruhr-uni-bochum.de/mpc/software/ProCon/index.html.en
Java based conversion tool for conversion of data from Proteomics files or a LIMS (Laboratory Information Management System) database into standard formats. Used to support wet-lab scientists in creating proteomics data files ready for upload into the public repositories.
Proper citation: ProCon - PROteomics CONversion (RRID:SCR_016363) 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://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://www.brainproducts.com/productdetails.php?id=21
Software for multifunctional recording designed to provide Brain Products GmbH- Solutions for Neurophysiological Research amplifier with a platform for recording setup and execution.
Proper citation: BrainVision Recorder (RRID:SCR_016331) Copy
https://www.adinstruments.com/products/dmt-normalization
Software tool for calculating optimal pretension conditions for microvascular or any small tubular tissue research. DMT Normalization Add-On, provided by ADInstruments, is included as part of LabChart Pro or can be purchased separately.
Proper citation: DMT Normalization (RRID:SCR_017024) 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://github.com/dvera/albacore
Data processing basecaller for the Oxford Nanopore sequencer that identifies DNA sequences directly from raw data. It enhances accuracy of the single-read sequence data, contributing to high consensus accuracy for nanopore sequence data.
Proper citation: Albacore (RRID:SCR_015897) Copy
https://github.com/eulerlab/QDSpy
Software Python tool for scripting and presenting stimuli for visual neuroscience.
Proper citation: QDSpy (RRID:SCR_016985) Copy
https://github.com/humanlongevity/HLA
Software tool for fast and accurate HLA typing from short read sequence data. Iteratively refines mapping results at amino acid level to achieve four digit typing accuracy for both class I and II HLA genes, taking only 3 min to process 30× whole genome BAM file on desktop computer.
Proper citation: xHLA (RRID:SCR_022277) Copy
https://www.gnu.org/software/sed/
Software tool as non interactive command line text editor. Command line that works with streams of characters for searching, filtering and text processing. Used for extracting part of file using pattern matching or substituting multiple occurrences of string within file.
Proper citation: GNU sed (RRID:SCR_018215) Copy
https://github.com/Brazelton-Lab/seq-annot
Software Python package for annotating and counting genomic features in genomes and metagenomes. Software tools to facilitate annotation and comparison of genomes and metagenomes.
Proper citation: seq-annot (RRID:SCR_018731) Copy
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