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http://www.swissdock.ch/

Web service to predict molecular interactions that may occur between target protein and small molecule. Protein small molecule docking web service based on EADock DSS.

Proper citation: SwissDock (RRID:SCR_022564) Copy   

•   Source: SciCrunch Registry

https://github.com/zdk123/SpiecEasi

Software R package for microbiome network analysis. Used for inference of microbial ecological networks from amplicon sequencing datasets. Combines data transformations developed for compositional data analysis with graphical model inference framework that assumes underlying ecological association network is sparse.

Proper citation: SpiecEasi (RRID:SCR_022712) Copy   

•   Source: SciCrunch Registry

https://github.com/jmchandonia/CORAL

Software tool as framework for rigorous self validated data modeling and integrative, reproducible data analysis.

Proper citation: CORAL (RRID:SCR_022711) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/SNPRelate/

Software R package as parallel computing toolset for relatedness and principal component analysis of SNP data.

Proper citation: SNPRelate (RRID:SCR_022719) Copy   

•   Source: SciCrunch Registry

https://github.com/Malindrie/scShapes

Software tool as statistical framework for identifying distribution shapes in single-cell RNA-sequencing data.

Proper citation: scShapes (RRID:SCR_022838) Copy   

•   Source: SciCrunch Registry

https://www.med.upenn.edu/ifi/cytofservicecenter.html

CyTOF�enables multi-parametric high-dimensional single�cell analysis�of more than 40 markers per cell, with�minimal background and compensation�issues.�Core�offers variety of�CyTOF-related services including�reagent distribution, consultation,�antibody conjugation, and data acquisition.�

Proper citation: University of Pennsylvania Perelman School of Medicine IFI CyTOF Service Center Core Facility (RRID:SCR_022410) Copy   

•   Source: SciCrunch Registry

https://github.com/axondeepseg/axondeepseg

Open source software tool for automatic axon and myelin segmentation from microscopy data using convolutional neural networks.

Proper citation: AxonDeepSeg (RRID:SCR_022531) Copy   

•   Source: SciCrunch Registry

http://rrwick.github.io/Bandage/

Software tool for visualising de novo assembly graphs. By displaying connections which are not present in contigs file, opens up new possibilities for analysing de novo assemblies. Used for interactive visualization of de novo genome assemblies.

Proper citation: Bandage (RRID:SCR_022772) Copy   

•   Source: SciCrunch Registry

https://github.com/xfengnefx/hifiasm-meta

Software tool as metagenome assembler that exploits high accuracy of recent data. De novo metagenome assembler, based on haplotype resolved de novo assembler for PacBio Hifi reads. Workflow consists of optional read selection, sequencing error correction, read overlapping, string graph construction and graph cleaning.

Proper citation: hifiasm-meta (RRID:SCR_022771) Copy   

•   Source: SciCrunch Registry

https://github.com/kimjh0107/22CellMorphologyLabelingTool

Software tool for image quality. Used for labeling quality of images and labeling center point of 3D RI images. Used to mange 3D RI cell images taken from holotomography.

Proper citation: Cell Morphology Labelling Tool (RRID:SCR_022770) Copy   

•   Source: SciCrunch Registry

https://github.com/bpucker/KIPEs

Software tool as automatic approach for identification of players in biosynthesis pathway. Used for automatic annotation of flavonoid biosynthesis steps in new transcriptome of genome sequence assembly. Various enzymes of entire metabolic networks can be identified if sufficient knowledge about functionally relevant amino acids is available.Combines comprehensive sequence similarity analyses with inspection of functionally relevant amino acid residues and domains in subjected peptide sequences.

Proper citation: Knowledge based Identification of Pathway Enzymes (RRID:SCR_022370) Copy   

•   Source: SciCrunch Registry

https://commons.cri.uchicago.edu/pcdc/

PCDC brings together clinical, genomic, and imaging data from institutions around the world to transform pediatric cancer research and outcomes. Headquartered at University of Chicago, PCDC works with international leaders in pediatric cancers and National Cancer Institute to develop and apply uniform data standards that facilitate collection, combination, and analysis of data from many different sources. PCDC Consortium developes common core data dictionary and common governance structure spanning pediatric cancers neuroblastoma, soft tissue sarcoma, acute myeloid leukemia, acute lymphoblastic leukemia, germ cell tumors, bone tumors, and Hodgkin lymphoma to enable innovative cross disease research as well as set standard for future cancer data commons endeavors.

Proper citation: Pediatric Cancer Data Commons (RRID:SCR_022369) Copy   

•   Source: SciCrunch Registry

https://napari.org/

Multi dimensional image viewer for Python. Used for browsing, annotating, and analyzing large multi dimensional images. Can be coupled to machine learning and image analysis tools enabling more user friendly automated analysis.

Proper citation: Napari (RRID:SCR_022765) Copy   

•   Source: SciCrunch Registry

https://gtca.github.io/muon/

Software Python framework designed to work with multimodal omics data. Aims to provide convenience and speed to its users enabling standardised analysis while staying flexible and expandable. Muon stands on shoulders of and integrates with annotated data object specification and scanpy library for single cell analysis in Python.

Proper citation: MUON (RRID:SCR_022804) Copy   

•   Source: SciCrunch Registry

https://github.com/ChristopherWilks/megadepth

Software tool for quantifying alignments and coverage for BigWig and BAM/CRAM input files.Quantifies number of RNA-seq reads assigned to gene in BAM file, successor of bamcounts.

Proper citation: Megadepth (RRID:SCR_022779) Copy   

•   Source: SciCrunch Registry

https://pmbb.med.upenn.edu/

BioBank supports researchers by providing centralized access to large number of annotated blood and tissue samples.

Proper citation: University of Pennsylvania Perelman School of Medicine Penn Medicine BioBank Core Facility (RRID:SCR_022415) Copy   

•   Source: SciCrunch Registry

https://github.com/Whitlock-Group/HERBS

Open source, extendable, intuitive and interactive software platform for image visualisation and image registration. Python based GUI for histological E-data registration in brain space.

Proper citation: Histological E data Registration in rodent Brain Spaces (RRID:SCR_022776) Copy   

•   Source: SciCrunch Registry

https://docs.airr-community.org/en/stable/datarep/rearrangements.html

Part of AIRR Data Model, defines annotations needed for rearrangements, which are sequences describing rearranged adaptive immune receptor chain (e.g., antibody heavy chain or TCR beta chain). Data for Rearrangement objects are stored as rows in tab delimited file and should be compatible with any TSV reader. Dataset is defined in this context as: TSV file, TSV with companion YAML file containing metadata, or directory containing multiple TSV files and YAML files.

Proper citation: Adaptive Immune Receptor Repertoire Rearrangement Schema (RRID:SCR_022592) Copy   

•   Source: SciCrunch Registry

https://orthovenn2.bioinfotoolkits.net/home

Web server for whole genome comparison and annotation of orthologous clusters across multiple species.Works on any operating system with modern browser and Javascript enabled. Used to identify orthologous gene clusters and supports user define species to upload customized protein sequences. Interactive graphic tool which provides Venn diagram view for comparing multiple species protein sequences.

Proper citation: OrthoVenn2 (RRID:SCR_022504) Copy   

•   Source: SciCrunch Registry

https://github.com/vdemichev/DiaNN

Software tool for processing of data independent acquisition proteomics experiments. Universal automated software suite for DIA proteomics data analysis. Neural networks and interference correction enable deep proteome coverage in high throughput.

Proper citation: DIA-NN (RRID:SCR_022865) Copy   

•   Source: SciCrunch Registry