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https://github.com/BodenmillerGroup/imctools
Software Python package that implements preprocessing pipeline for imaging mass cytometry data. Can convert IMC raw files to tiff files that are used as inputs into CellProfiller, Ilastik, Fiji etc.
Proper citation: imctools (RRID:SCR_017132) Copy
https://bitbucket.org/mroachawri/purge_haplotigs/src
Pipeline for reassigning primary contigs that should be labelled as haplotigs. Used for third generation sequencing based assemblies to automate reassignment of allelic contigs, and to assist in manual curation of genome assemblies.
Proper citation: Purge_haplotigs (RRID:SCR_017616) Copy
https://github.com/colinvaz/nmf-toolbox
Software toolbox for performing Non-negative Matrix Factorization (NMF) and several variants. Used to factorize one non negative matrix into two non negative factors, that is basis matrix and coefficient matrix. Applied in bioinformatics as data mining approach.
Proper citation: NMF Toolbox (RRID:SCR_017069) 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
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
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/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
https://www.ncbi.nlm.nih.gov/UniGene/help.cgi?item=DDD
Software tool for comparing EST profiles in order to identify genes with significantly different expression levels.
Proper citation: Digital Differential Display (DDD) (RRID:SCR_016638) 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://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://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/lufuhao/ExonerateTransferAnnotation
Software tool as pipeline to make anntotations using cDNA and CDS sequences.
Proper citation: ExonerateTransferAnnotation (RRID:SCR_017557) Copy
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