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https://github.com/Danko-Lab/dREG

Software tool for detecting regulatory elements using GRO-seq and PRO-seq.

Proper citation: dREG (RRID:SCR_027012) Copy   

•   Source: SciCrunch Registry

https://www.bcm.edu/research/atc-core-labs/mass-spectrometry-proteomics-core

Core provides services including project evaluation and design, sample processing and biochemical purifications, mass spectrometry measurements, data processing, and bioinformatics analysis performed by the experienced core personnel.

Proper citation: Baylor College of Medicine BCM Mass Spectrometry Proteomics Core Facility (RRID:SCR_027015) Copy   

•   Source: SciCrunch Registry

https://apps.cytoscape.org/apps/yfileslayoutalgorithms

Software suite of algorithms used for arranging and visualizing graph structures. They provide variety of layout styles, such as hierarchical, organic, tree, circular, and orthogonal, each optimizing for different criteria and visualization needs.

Proper citation: yFiles Layout Algorithms (RRID:SCR_026961) Copy   

•   Source: SciCrunch Registry

https://github.com/steineggerlab/foldseek

Software tool for fast and sensitive comparisons of large structure sets. Used for comparisons of large protein structure sets, supporting monomer and multimer searches, as well as clustering. It runs on CPU, supports GPU acceleration for faster searches, and optionally allows ultra-fast and sensitive comparisons directly from protein sequence inputs using a language model, bypassing the need for structures.

Proper citation: Foldseek (RRID:SCR_027018) Copy   

•   Source: SciCrunch Registry

https://github.com/Rosemeis/pcangsd

Software framework for analyzing low-depth next-generation sequencing data in heterogeneous/structured populations using principal component analysis.

Proper citation: pcangsd (RRID:SCR_026956) Copy   

•   Source: SciCrunch Registry

https://bitbucket.org/tguenther/read/src/master/

Software tool to infer family relationships for degraded samples. Used to infer degree of relationship (up to second degree, i.e. nephew/niece-uncle/aunt, grandparent-grandchild or half-siblings) for pair of low-coverage individuals.

Proper citation: READ (RRID:SCR_026958) Copy   

•   Source: SciCrunch Registry

https://github.com/BigDataBiology/SemiBin/

Software command tool for metagenomic binning with deep learning, handles both short and long reads. Used for metagenomic binning at contig level which uses deep contrastive learning.

Proper citation: SemiBin (RRID:SCR_026896) Copy   

•   Source: SciCrunch Registry

https://github.com/chklovski/CheckM2

Software tool to predict completeness and contamination of genomic bins. Used for predicting genome quality of metagenome-assembled genomes. Assessing microbial genome quality using machine learning.

Proper citation: CheckM2 (RRID:SCR_026897) Copy   

•   Source: SciCrunch Registry

https://github.com/grimme-lab/xtb

Software semiempirical extended tight-binding program package. Provides userfriendly interface for performing geometry optimizations, vibrational frequency calculations, and Molecular Dynamics simulations.

Proper citation: xTB (RRID:SCR_026929) Copy   

•   Source: SciCrunch Registry

https://github.com/qcxms/QCxMS

Software application as quantum chemical based program that enables users to calculate mass spectra using Born-Oppenheimer Molecular Dynamics. Quantum mechanic mass spectrometry calculation program.

Proper citation: QCxMS (RRID:SCR_026928) Copy   

•   Source: SciCrunch Registry

https://github.com/OpenTOPAS/OpenTOPAS

Software Monte Carlo tool for particle simulation. Used for simulation of medical applications of ionizing radiation with the Monte Carlo method. Allows to assemble and control library of simulation objects (geometry components, particle sources, scorers, etc.) with no need to write C++ code and without knowledge of underlying Geant4 Simulation Toolkit.

Proper citation: OpenTOPAS (RRID:SCR_026927) Copy   

•   Source: SciCrunch Registry

https://www.cogentech.it/genomic_unit.php

Cogentech's Genomic Core Facility (GU) provides professional support for workflow of research projects, from counseling on experimental design to functional interpretation of results. Support includes identification of the most suitable methodology to achieve the experimental aim, quality control of nucleic acid, generation of indexed fragment library, sequencing according to experimental needs and bioinformatic support for selected applications. Customized protocols can be set-up as well. Sequencing data are delivered using a password protected user-friendly web interface. The laboratory is ISO9001 certified.

Proper citation: IFOM ETS Cogentech GU Genomics Core Facility (RRID:SCR_026935) Copy   

•   Source: SciCrunch Registry

https://www.cogentech.it/histology.php

Cogentech's Histopathology (HP) Core Facility provides services including consultation, tissue trimming and embedding, cutting, staining, photographic documentation for the evaluation and characterization of normal and pathological tissues. Provides Optimization of protocols for new stains or biological specimen.The laboratory is ISO9001 certified.

Proper citation: IFOM ETS Cogentech HP Histopathology Core Facility (RRID:SCR_026934) Copy   

•   Source: SciCrunch Registry

https://www.mclaughlinresearch.org/gemma-core-2

GEMMA Core offers transgenic and genotyping services needed for experiments, phenotyping and behavioral services, and mouse colony management services to COBRE faculty. Consultation and training for lab staff is also available.

Proper citation: McLaughlin Research Institute Gene Editing and Mouse Models Assessment Core Facility (RRID:SCR_027045) Copy   

•   Source: SciCrunch Registry

https://www.augusta.edu/cancer/research/shared-resources/small-animal/

Core provides preclinical imaging and radiation treatment resources for animal research.

Proper citation: Augusta University GCC Small Animal Imaging Core Facility (RRID:SCR_027047) Copy   

•   Source: SciCrunch Registry

https://www.obio-tech.com/

Established in 2013, OBiO Technology（Shanghai）Corp.,Ltd. is Contract Research Organization and Contract Development and Manufacturing Organization in cell and gene therapy. Provides technical services for the field of Regenerative Medicine and Anti-aging, including cell preparation, production of recombinant proteins/exosomes, and cell storage.

Proper citation: OBiO Technology (RRID:SCR_027205) Copy   

•   Source: SciCrunch Registry

https://github.com/gevaertlab/DUNE

Software tool to extract low-dimensional deep features from multisequence brain MRI data using unsupervised autoencoders.

Proper citation: GevaertLab_DUNE (RRID:SCR_027208) Copy   

•   Source: SciCrunch Registry

https://hasindu2008.github.io/slow5specs/

File format for storing signal data from Oxford Nanopore Technologies sequencing devices. SLOW5 can be encoded in human-readable ASCII format, or more compact and efficient binary format (BLOW5) - this is analogous to the seminal SAM/BAM format for storing DNA sequence alignments.

Proper citation: slow5 format (RRID:SCR_027155) Copy   

•   Source: SciCrunch Registry

https://github.com/hasindu2008/f5c/

Software ultra-fast methylation calling and event alignment tool for nanopore sequencing data (supports CUDA acceleration).

Proper citation: f5c (RRID:SCR_027158) Copy   

•   Source: SciCrunch Registry

https://github.com/mskilab-org/gGnome

Software package provides flexible, queriable R interface to graphs and walks of reference genomic intervals. gGnome is written in R6 object oriented standard and built around GenomicRanges, data.table, and igraph backend, and thus supports agile interaction with graphs consisting of hundreds of thousands of nodes and edges.

Proper citation: gGnome (RRID:SCR_027150) Copy   

•   Source: SciCrunch Registry