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https://github.com/Optophys-Lab/FreiBox/tree/main/Commutator_FreiBox2022

Affordable commutator that is equipped with novel sensing system that improves online tracking of cable rotations without impairing the 1-photon calcium imaging via Miniscope. Commutator to allow freely moving behaviors while recording neural activity from platforms such as Miniscope V4 and OpenEphys. Used to perform calcium imaging.

Proper citation: commutator (RRID:SCR_023919) Copy   

•   Source: SciCrunch Registry

https://github.com/Optophys-Lab/FreiBox

Versatile open source behavioral system for investigating neuronal correlates of behavioral flexibility via 1-Photon Imaging in freely moving mice. Behavioral testing platform consists of FreiBox, novel low-cost Arduino behavioral setup, controlled by custom Python interface and integrates new licking sensor (strain gauge lickometer) for controlling spatial licking behavioral tasks.

Proper citation: Freibox (RRID:SCR_023918) Copy   

•   Source: SciCrunch Registry

https://github.com/jkbonfield/htscodecs/

Software repository implements the custom CRAM codecs used for "EXTERNAL" block types.Custom compression for CRAM custom algorithm written to compress the BAM file format for DNA sequencing data.

Proper citation: Htscodecs (RRID:SCR_024034) Copy   

•   Source: SciCrunch Registry

https://github.com/conda/conda-package-handling

Software to create and extract conda packages of various formats.

Proper citation: conda-package-handling (RRID:SCR_023991) Copy   

•   Source: SciCrunch Registry

http://www.cbcb.umd.edu/software/ELPH/index.shtml

Software tool as general purpose Gibbs sampler for finding motifs in set of DNA or protein sequences.Takes as input a set containing sequences, and searches through them for the most common motif, assuming that each sequence contains one copy of the motif. Used to find patterns such as ribosome binding sites (RBSs) and exon splicing enhancers (ESEs).

Proper citation: ELPH (RRID:SCR_024011) Copy   

•   Source: SciCrunch Registry

https://gitlab.com/tjobbertjob/ms-review-paper

Variability analysis of proteomics data used for deep learning.

Proper citation: ms-variability-analysis (RRID:SCR_024531) Copy   

•   Source: SciCrunch Registry

https://github.com/PacificBiosciences/unanimity

Software to generate highly accurate single molecule consensus reads.

Proper citation: CCS (RRID:SCR_024379) Copy   

•   Source: SciCrunch Registry

https://github.com/cancerit/alleleCount

Software package to prevent code duplication. Support code for NGS copy number algorithms. Generates count of coverage of each allele ACGT at that location given any filter settings.

Proper citation: alleleCount (RRID:SCR_023961) Copy   

•   Source: SciCrunch Registry

https://github.com/ejcorn/mouse_abi_tool

Software tool to pull gene expression from Allen Brain Institute API in same annotation space as structural connectome.

Proper citation: Mouse_abi_tool (RRID:SCR_023831) Copy   

•   Source: SciCrunch Registry

https://github.com/mateidavid/fast5

Software C++ library for accessing Oxford Nanopore Technologies sequencing data.

Proper citation: Fast5 Library (RRID:SCR_024023) Copy   

•   Source: SciCrunch Registry

https://github.com/TADA-A/TADA-A/tree/master

Software statistical framework for mapping risk genes from de novo mutations in whole genome sequencing studies.

Proper citation: TADA-A (RRID:SCR_024538) Copy   

•   Source: SciCrunch Registry

https://github.com/VioletteChiara/AnimalTA

Software video tracking tool for tracking and analysing animal movement in different environments.

Proper citation: AnimalTA (RRID:SCR_023784) Copy   

•   Source: SciCrunch Registry

https://biom-format.org/

Software provides command line interface and Python API for working with Biological Observation Matrix files.

Proper citation: python-biom-format (RRID:SCR_024193) Copy   

•   Source: SciCrunch Registry

https://github.com/opensafely-core

The code that runs the OpenSAFELY platform used for analysis of electronic health records data.

Proper citation: OpenSAFELY (RRID:SCR_023790) Copy   

•   Source: SciCrunch Registry

https://github.com/liqihang007/VIS_STEB

Web based visual analytics tool for the comprehensive exploration of genomic and phenotypic patterns, especially for the spatiotemporal patterns, in the developing mouse brain. The tool is designed in JavaScript and D3.js, the data is based on Allen Developing Mouse Brain Atlas (ADMBA) data.

Proper citation: Spatiotemporal pattern Exploration of Brain (RRID:SCR_023825) Copy   

•   Source: SciCrunch Registry

http://bioinf.cs.ucl.ac.uk/downloads/MetaPSICOV/

Software tool for accurate prediction of contacts and long range hydrogen bonding in proteins.

Proper citation: MetaPSICOV (RRID:SCR_024517) Copy   

•   Source: SciCrunch Registry

https://github.com/PapenfussLab/DMS_with_Alanine_scan

Code used for data processing, variant impact predictor modelling and result analysis. Used to improve prediction results to predict the impact of amino acid variants. Extended linear regression-based predictor to explore whether incorporating data from alanine scanning, widely-used low-throughput mutagenesis method, would improve prediction results.

Proper citation: DMS_with_Alanine_scan (RRID:SCR_023949) Copy   

•   Source: SciCrunch Registry

https://scikit-learn.org/stable/modules/generated/sklearn.svm.LinearSVC.html

Software application for linear support vector classification. Used in classification problems.

Proper citation: LinearSVC (RRID:SCR_024741) Copy   

•   Source: SciCrunch Registry

https://github.com/CahanLab/singleCellNet

Software tool to classify single cell RNA-Seq data across platforms and across species.

Proper citation: SingleCellNet (RRID:SCR_024742) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/org.Hs.eg.db/

Software R package as object for simple mapping of Entrez Gene identifiers https://www.ncbi.nlm.nih.gov/ entrez/query.fcgi?db=gene to all possible GenBank accession numbers.

Proper citation: org.Hs.eg.db (RRID:SCR_024739) Copy   

•   Source: SciCrunch Registry