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Operant Box code
Proper citation: pyOS-5 (RRID:SCR_022336) Copy
https://github.com/2019surbhi/tinglab_ureter_analysis/tree/v1
Analysis code relevant to scRNA sequencing analysis. Code for Fink and Sona et.al. (2022) publication.
Proper citation: tinglab ureter analysis (RRID:SCR_022525) Copy
https://bioconductor.org/packages/FlowSorted.Blood.EPIC/
Software package includes new cell reference for adult peripheral blood deconvolution arrayed using Illumina HumanMethylationEPIC.Optimized library for reference based deconvolution of whole blood biospecimens assayed using Illumina HumanMethylationEPIC BeadArray.
Proper citation: FlowSorted.Blood.EPIC (RRID:SCR_022540) Copy
https://github.com/AlgoLab/CouGaR-g
Source code for "Accurate and Fast Clade Assignment via Deep Learning and Frequency Chaos Game Representation".
Proper citation: CouGaR-g (RRID:SCR_022952) Copy
https://github.com/shooshtarilab/Subsemble_Cell_Type_Classifier
Supervised ensemble machine learning classifier. Classification performance benchmark scripts.
Proper citation: Subsemble Cell Type Classifier (RRID:SCR_022784) Copy
https://github.com/protofilamentdude/Protofilament-Bending-Models
Code is written to be run with Matlab version r2020b or higher. Model accepts wave assay pulse amplitude data, and simultaneously solves and fits protofilament deflection models to deduce fundamental biophysical properties of microtubule protofilaments.
Proper citation: Protofilament Bending Models (RRID:SCR_023062) Copy
https://github.com/caraweisman/abSENSE
Software to interpret undetected homolog.Method that calculates probability that homolog of given gene would fail to be detected by homology search in given species, even if homolog were present and evolving normally.
Proper citation: abSENSE (RRID:SCR_023223) Copy
https://github.com/compbiolabucf/PTNet
Graph based learning model for protein expression estimation by considering miRNA-mRNA interactions. Estimates protein levels by considering miRNA-mRNA interaction network, mRNA expression and miRNA expression.
Proper citation: PTNet (RRID:SCR_022975) Copy
https://github.com/DeNardoLab/BehaviorDEPOT
Software tool for automated behavioral detection based on markerless pose tracking. Behavioral analysis tool to first compile and clean point-tracking output from DeepLabCut, and then classify behavioral epochs using custom behavior classifiers. Used to detect frame by frame behavior from video time series and can analyze results of common experimental assays, including fear conditioning, decision-making in T-maze, open field, elevated plus maze, and novel object exploration. Calculates kinematic and postural statistics from keypoint tracking data from pose estimation software outputs.
Proper citation: BehaviorDEPOT (RRID:SCR_023602) Copy
https://github.com/DigitalHealthcareLab/22ActionRecognitionTool
Software tool for multi view child motor development dataset for AI-driven assessment of child development project.
Proper citation: 22ActionRecognitionTool (RRID:SCR_023552) Copy
https://github.com/fhcrc/seqmagick/
Software application to expose file format conversion in BioPython in convenient way. Imagemagick like frontend to Biopython SeqIO.
Proper citation: seqmagick (RRID:SCR_024331) Copy
https://github.com/WorkflowConversion/CTDopts
Software gives your command-line tools a CTD-compatible interface. Module for enabling tools with CTD reading/writing, argument parsing, validating and manipulating capabilities.
Proper citation: CTDopts (RRID:SCR_023997) Copy
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
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
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
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
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
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
https://github.com/PacificBiosciences/unanimity
Software to generate highly accurate single molecule consensus reads.
Proper citation: CCS (RRID:SCR_024379) Copy
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
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