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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://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://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
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
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/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
Software interface to use R from Python.
Proper citation: rpy2 (RRID:SCR_024701) 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/mateidavid/fast5
Software C++ library for accessing Oxford Nanopore Technologies sequencing data.
Proper citation: Fast5 Library (RRID:SCR_024023) Copy
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
Software provides command line interface and Python API for working with Biological Observation Matrix files.
Proper citation: python-biom-format (RRID:SCR_024193) Copy
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
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
https://github.com/amathislab/DeepDraw
Software application for creating scalable muscle spindles dataset based on kinematic data and define action recognition task as benchmark. Training and analysis of hierarchical neural networks to solve recognition task from muscle spindle inputs.
Proper citation: DeepDraw (RRID:SCR_024840) Copy
https://github.com/liufan-creat/bulkGAN
Software tool for scRNA and spatial transcriptomics.Used to generate RNA data close to real bulk RNA-seq with constraints of scRNA-seq data, based on keras and tensflow framework.
Proper citation: bulkGAN (RRID:SCR_024798) Copy
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
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
https://cellxgene.cziscience.com/
Portal used to find and download any of data sets published on CELLxGENE. Allows to download and visually explore data to understand functionality of human tissues at cellular level. Optimized for finding, exploring, and reusing single cell data. Collections Page lists collections hosted on CELLxGENE Discover and metadata that define tissue, assay, disease, organism, and cell count for each collection. Once you find published dataset of interest on CELLxGENE Discover, you can click on the explore button below the dataset description to explore the cells of that dataset using the CELLxGENE Explorer.
Proper citation: CZ CELLxGENE Discover (RRID:SCR_024894) Copy
https://www.adobe.com/ca/products/fresco.html
Software digital painting and drawing application. Used to create figures. Built for the latest stylus and touch devices, now including iPhones. Collection of vector and raster brushes, live brushes, to deliver natural painting and drawing experience.Vector and raster graphics editor developed by Adobe primarily for digital painting. Originally designed for the Apple iPad with Pencil support.
Proper citation: Adobe Fresco (RRID:SCR_024887) Copy
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