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https://github.com/c-zhou/yahs

Software command line tool for construction of chromosome scale scaffolds from Hi-C data. Scaffolding tool using Hi-C or Omni-C data. Used to scaffold contig level assemblies into chromosome scale scaffolded assemblies.

Proper citation: YaHS (RRID:SCR_022965) Copy   

•   Source: SciCrunch Registry

http://tiger.bsc.es

Resource enables integrative exploration of genetic and epigenetic basis of development of Type 2 Diabetes, together with other associated functional, molecular and clinical data, centered in biology and role of pancreatic beta cells.The gene expression regulatory variation landscape of human pancreatic islets.

Proper citation: TIGER Data Portal (RRID:SCR_023626) Copy   

•   Source: SciCrunch Registry

https://github.com/mskcc/lohhla

Software tool to evaluate HLA loss using next-generation sequencing data. Computational tool to determine HLA allele-specific copy number from sequencing data.

Proper citation: LOHHLA (RRID:SCR_023690) Copy   

•   Source: SciCrunch Registry

http://www.alspac.bris.ac.uk

A long-term health research project which follows pregnant women and their offspring in a continuous health and developmental study. More than 14,000 mothers enrolled during pregnancy in 1991 and 1992, and the health and development of their children has been followed in great detail. The ALSPAC families have provided a vast amount of genetic and environmental information over the years which can be made available to researchers globally.

Proper citation: ALSPAC (RRID:SCR_007260) Copy   

•   Source: SciCrunch Registry

http://www.opensourcebrain.org

A resource for sharing and collaboratively developing computational models of neural systems. While models can be submitted and developed in any format, the use of open standards such as NeuroML and PyNN is encouraged, to ensure transparency, modularity, accessibility and cross simulator portability. OSB will provide advanced facilities to analyze, visualize and transform models in these formats, and to connect researchers interested in models of specific neurons, brain regions and disease states. Research themes include: Basal ganglia modelling, Cerebellar Granule cell modelling, Cerebellar modelling, Hippocampal modelling, Neocortical modelling, Whole brain models. Additional themes are welcome.

Proper citation: Open Source Brain (RRID:SCR_001393) Copy   

•   Source: SciCrunch Registry

http://www.ucl.ac.uk/ploras#annotations:QXuC2C7REeaxtw-aEPo07Q

A research project investigating the difficulties of recovering language after stroke (aphasia). The overall aim of the study is to give future stroke survivors accurate predictions of their aphasia recovery by creating clinical tools and discerning why some patients recover from aphasia better than others.

Proper citation: Predicting Language Outcome and Recovery After Stroke (PLORAS) (RRID:SCR_014498) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://hmri.info

Software toolbox for quantitative MRI in neuroscience and clinical research. Open source and flexible tool for qMRI data handling and processing. Allows estimation of high quality multi parameter qMRI maps followed by spatial registration in common space for statistical analysis.

Proper citation: hMRI-toolbox (RRID:SCR_017682) Copy   

•   Source: SciCrunch Registry

https://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/balbes/balbes_layout.html

Software system for solving protein structures using x-ray crystallographic data. Automatic molecular replacement pipeline for molecular replacement in CCP4. Integrates into one system all components necessary for solving crystal structure by Molecular Replacement. System is automated so that it needs no user intervention when running combination of jobs such as model searching, molecular replacement and refinement.

Proper citation: BALBES (RRID:SCR_018763) Copy   

•   Source: SciCrunch Registry

http://crosslinkviewer.org/

Open source web based visualization tool for exploring crosslinking mass spectrometry results. Displays residue resolution positional information including linkage sites and linked peptides, all types of crosslinking reaction product, ambiguous results and additional sequence information such as domains.

Proper citation: xiNET (RRID:SCR_021010) Copy   

•   Source: SciCrunch Registry

http://www.hipsci.org/

A UK national induced pluripotent stem (iPS) cell resource that will create and characterize more than 1000 human iPSCs from healthy and diseased tissue for use in cellular genetic studies. Between 2013 and 2016 they aim to generate iPS cells from over 500 healthy individuals and 500 individuals with genetic disease. They will then use these cells to discover how genomic variation impacts on cellular phenotype and identify new disease mechanisms. Strong links with NHS investigators will ensure that studies on the disease-associated cell lines will be linked to extensive clinical information. Further key features of the project are an open access model of data sharing; engagement of the wider clinical genetics community in selecting patient samples; and provision of dedicated laboratory space for collaborative cell phenotyping and differentiation.

Proper citation: HipSci (RRID:SCR_003909) Copy   

•   Source: SciCrunch Registry

http://www.sanger.ac.uk/mouseportal/

Database of mouse research resources at Sanger: BACs, targeting vectors, targeted ES cells, mutant mouse lines, and phenotypic data generated from the Institute''''s primary screen. The Wellcome Trust Sanger Institute generates, characterizes, and uses a variety of reagents for mouse genetics research. It also aims to facilitate the distribution of these resources to the external scientific community. Here, you will find unified access to the different resources available from the Institute or its collaborators. The resources include: 129S7 and C57BL6/J bacterial artificial chromosomes (BACs), MICER gene targeting vectors, knock-out first conditional-ready gene targeting vectors, embryonic stem (ES) cells with gene targeted mutations or with retroviral gene trap insertions, mutant mouse lines, and phenotypic data generated from the Institute''''s primary screen.

Proper citation: Sanger Mouse Resources Portal (RRID:SCR_006239) Copy   

•   Source: SciCrunch Registry

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

Software tool to improve sensitivity, objectivity and interpretability of analysis of multi-subject diffusion imaging studies.

Proper citation: Tract Based Spatial Statistics (RRID:SCR_024932) Copy   

•   Source: SciCrunch Registry

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

Software command line tool for automated tractography. Standardised protocols for automated tractography in human and macaque brain.

Proper citation: XTRACT (RRID:SCR_024933) Copy   

•   Source: SciCrunch Registry

https://brainlife.io/docs/using_ezBIDS/

Web-based BIDS conversion tool to convert neuroimaging data and associated metadata to BIDS standard. Guided standardization of neuroimaging data interoperable with major data archives and platforms.

Proper citation: ezBIDS (RRID:SCR_025563) Copy   

•   Source: SciCrunch Registry

https://tristanic.github.io/isolde/

Software environment to ease task of building macromolecular models into low to medium resolution experimental maps. Physically realistic environment for model building into low-resolution electron-density maps. Can generate maps directly from crystallographic F/sigF data in MTZ format and automatically re-calculate them when model changes, and/or generate "static" maps from pre-calculated F/phi data.

Proper citation: ISOLDE (RRID:SCR_025577) Copy   

•   Source: SciCrunch Registry

https://www.ucl.ac.uk/biosciences/research/research-facilities/molecular-biology/darwin-research-facility-drf

Facility provides diverse range of equipment, expertise and training in field of biochemistry, molecular, structural and cellular biology. Facility consists of several research laboratories and support areas.

Proper citation: University College London Darwin Research Core Facility (RRID:SCR_026345) Copy   

•   Source: SciCrunch Registry

https://github.com/aametwally/Metabolic_Subphenotype_Predictor

Software repository contains code for Inference of T2D metabolic subphenotypes (MuscleIR, Beta-cell Function, Incretin Effect, Hepatic IR), Identification of dominant metabolic subphenotype, Feature extraction from glucose tiemseries, Extraction of reduced representation of glucose tiemseries,Visualization of metabolic phenotypes based on various glucose-related metrics,Concordance between CGM and Venous glucose values from at home and at clinical setting, Classification of metabolic subphenotypes.

Proper citation: Metabolic Subphenotype Predictor (RRID:SCR_027192) Copy   

•   Source: SciCrunch Registry

https://github.com/wheaton5/souporcell

Software tool to cluster cells using the genetic variants detected within the scRNAseq reads. Robust clustering of single-cell RNA-seq data by genotype without reference genotypes. Used for clustering scRNAseq by genotypes.

Proper citation: Souporcell (RRID:SCR_027462) Copy   

•   Source: SciCrunch Registry

https://github.com/Core-Bioinformatics/bulkAnalyseR

Software R package for most bulk sequencing datasets. Creates shiny app for interactive data analysis and visualisation. Used for analysing and sharing bulk sequencing results.

Proper citation: bulkAnalyseR (RRID:SCR_027647) Copy   

•   Source: SciCrunch Registry