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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

https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/MCFLIRT

Software intra-modal motion correction tool designed for use on fMRI time series for linear (affine) inter- and inter-modal brain image registration.

Proper citation: MCFLIRT (RRID:SCR_024792) Copy   

•   Source: SciCrunch Registry

https://github.com/SlicerMorph/SlicerMorph

Open and extensible platform to retrieve, visualize and analyse 3D morphology.Extension to import microCT data and conduct 3D morphometrics in Slicer. Used for data import, visualization, measurement, annotation, and geometric morphometric analysis on 3D data, including volumetric scans (CTs and MRs) and 3D surface scans, all within the 3D Slicer application.

Proper citation: SlicerMorph (RRID:SCR_024674) Copy   

•   Source: SciCrunch Registry

https://rpy2.github.io/

Software interface to use R from Python.

Proper citation: rpy2 (RRID:SCR_024701) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/ggbreak/vignettes/ggbreak.html

Software package provides several scale functions to break down ‘gg’ plot into pieces and align them together with gap plot or without (wrap plot or cut plot) ignoring subplots. Package was first designed to set breakpoints for truncating plot to shrink outlier long branch of phylogenetic tree. Set Axis Break for ggplot2.

Proper citation: ggbreak (RRID:SCR_024824) Copy   

•   Source: SciCrunch Registry

https://github.com/holab-hku/Vulture

Software scalable cloud based pipeline that performs microbial calling for single cell RNA sequencing data, enabling meta analysis of the single cell host microbial studies from AWS Open Data and other public domain.

Proper citation: Vulture (RRID:SCR_024720) Copy   

•   Source: SciCrunch Registry

https://github.com/mcelotto/Feature_Info_Transfer

Software application as MATLAB scripts to compute measures of Feature-specific Information Transfer (FIT) and conditional FIT (cFIT). FIT quantifies direction and magnitude of information flow about specific feature S (such as feature of sensory stimulus) between simultaneously recorded brain regions X and Y. cFIT quantifies amount of directed feature information transmitted between regions X and Y that cannot be potentially routed through region Z.

Proper citation: Feature-specific Information Transfer scripts (RRID:SCR_024772) Copy   

•   Source: SciCrunch Registry

https://github.com/mcelotto/LemkeCelottoEtAl_codes_repo

Software code package associated to the paper: Lemke et al. Information flow between motor cortex and striatum reverses during skill learning. 2023. Quantifies information theoretic quantities used in the associated study.

Proper citation: LemkeCelottoEtAl_codes_repo (RRID:SCR_024773) Copy   

•   Source: SciCrunch Registry

https://github.com/broadinstitute/ichorCNA

Software tool that quantifies tumor content in cfDNA from 0.1× coverage whole-genome sequencing data without prior knowledge of tumor mutations. Used to simultaneously segment genome, predict large scale copy number alterations, and estimate tumor fraction of ultra low pass whole genome sequencing sample.

Proper citation: ichorCNA (RRID:SCR_024768) Copy   

•   Source: SciCrunch Registry

https://github.com/STOmics/SGAE

Software graph neural network based tool for spatial domain deciphering. Used for deciphering spatial domains from spatially resolved transcriptomics.

Proper citation: SGAE (RRID:SCR_024803) Copy   

•   Source: SciCrunch Registry

https://github.com/google-deepmind/deepmind-research/tree/master/enformer

Software package provides implementation of the Enformer model and examples on running the model.

Proper citation: Enformer (RRID:SCR_024805) Copy   

•   Source: SciCrunch Registry

https://github.com/kundajelab/tfmodisco

Software application as algorithm for identifying motifs from basepair-level importance scores computed on genomic sequence data.

Proper citation: TF-Modisco (RRID:SCR_024811) Copy   

•   Source: SciCrunch Registry

https://github.com/PaulingLiu/scibet

Software tool as supervised cell type identifier that accurately predicts cell identity for newly sequenced single cells.

Proper citation: SciBet (RRID:SCR_024743) Copy   

•   Source: SciCrunch Registry

https://www.tidyverse.org/blog/2018/11/parsnip-0-0-1/

Software R package to create and manipulate functions commonly used during modeling e.g. fitting the model, making predictions, etc.

Proper citation: Parsnip (RRID:SCR_024744) Copy   

•   Source: SciCrunch Registry

http://lfpy.github.io

Python package for calculation of extracellular potentials from multicompartment neuron models. LFPy can be used to set up a model, run simulations, and calculate the extracellular potentials arising from activity in the given model neuron. It relies on the Python interface provided by the NEURON simulator.

Proper citation: LFPy (RRID:SCR_014805) Copy   

•   Source: SciCrunch Registry

http://www.msg.chem.iastate.edu/gamess/

Software program for ab initio molecular quantum chemistry. GAMESS can compute SCF wavefunctions ranging from RHF, ROHF, UHF, GVB, and MCSCF. Capabilities include using nuclear gradients for automatic geometry optimization, modeling of solvent effects, computation of the energy hessian for prediction of vibrational frequencies, as well as computation of nuclear wavefunctions. The program can also compute variety of molecular properties, ranging from simple dipole moments to frequency dependent hyperpolarizabilities.

Proper citation: Gamess (RRID:SCR_014896) Copy   

•   Source: SciCrunch Registry

http://bioc.sourceforge.net

An interchange format to represent, store and exchange data and annotations in a standardized manner.

Proper citation: BioC Java Library (RRID:SCR_014777) Copy   

•   Source: SciCrunch Registry