Tools   Select Another Resource Report Type

https://github.com/gtonkinhill/panaroo

Software pipeline for pangenome investigation. Shares information between genomes to correct errors. Can call large structural variants.Fast and scalable to over 10k bacterial genomes.

Proper citation: Panaroo (RRID:SCR_021090) Copy   

•   Source: SciCrunch Registry

https://github.com/Benson-Genomics-Lab/TRF

Software tool to locate and display tandem repeats in DNA sequences. Used to analyze DNA sequences.

Proper citation: Tandem Repeats Finder (RRID:SCR_022065) Copy   

•   Source: SciCrunch Registry

http://neomorph.salk.edu/omb/

Viewer for DNA Methylation Atlas of Mouse Brain at Single Cell Resolution. Browser to interactively explore single cell methylome dataset including exploration of methylation diversity of one gene at single-cell or cell-type level, exploration of cell type composition of adult mouse brain dissection regions and anatomical structures, explorartion of spatial distribution and methylation signature genes of one cell type.

Proper citation: Brain Cell Methylation Viewer (RRID:SCR_020954) Copy   

•   Source: SciCrunch Registry

http://old.protein.bio.unipd.it/cspritz/

Web tool for prediction of intrinsic protein disorder segments with annotation for homology, secondary structure and linear motifs.

Proper citation: CSpritz (RRID:SCR_021884) Copy   

•   Source: SciCrunch Registry

https://signor.uniroma2.it/

Software application to organize and store in structured format signaling information published in scientific literature. Information is stored as binary causative relationships between biological entities and can be represented graphically as activity flow. Each relationship is linked to literature reporting experimental evidence. Each node is annotated with chemical inhibitors that modulate its activity. Signaling information is mapped to human proteome. SIGNOR 2.0 stores manually annotated causal relationships between proteins and other biologically relevant entities including chemicals, phenotypes, complexes, etc with compliance to FAIR data principles.

Proper citation: SIGNOR (RRID:SCR_018485) Copy   

•   Source: SciCrunch Registry

https://pathology.med.upenn.edu/research/core-resources/tumor-tissue-biospecimen-bank

Centralized biorepository of human biosamples. TTAB is responsible for the collection, processing, and storage of human blood, fluid, and tissue at the University of Pennsylvania Health System. TTAB has a collection bench within Surgical Pathology Suite at Hospital of University of Pennsylvania (HUP).� Our collection bench sits adjacent to frozen section teams managing clinical sample collection and allowing for tight integration of tissue sample collection with clinical pathology teams.

Proper citation: University of Pennsylvania Perelman School of Medicine Tumor Tissue Biospecimen Bank Core Facility (RRID:SCR_022430) Copy   

•   Source: SciCrunch Registry

https://github.com/mueller-lab/PyFRAP

Software Python package for FRAP analysis. Simulation based analysis software that makes use of PDE simulations to analyze FRAP experiments in 3D geometries. Used to assess molecular diffusion.

Proper citation: PyFRAP (RRID:SCR_022665) Copy   

•   Source: SciCrunch Registry

https://github.com/holmescao/ANTS_marking_and_analysis_tools

Software tool for marking ant motion trajectories dataset from video. Provided marking software, three data quality analysis scripts, and tracking performance evaluation tool.

Proper citation: ANTS marking and analysis tools (RRID:SCR_022543) Copy   

•   Source: SciCrunch Registry

https://github.com/mueller-lab/PyFDAP

Software tool as automated analysis of fluorescence decay after photoconversion (FDAP) experiments.

Proper citation: PyFDAP (RRID:SCR_022664) Copy   

•   Source: SciCrunch Registry

https://ibidi.com/chemotaxis-analysis/171-chemotaxis-and-migration-tool.html?gclid=CjwKCAjwu5yYBhAjEiwAKXk_eOEiTG2oTzme7pgYbZus8ZBKhu4S8YCWwlbQdQLdcOTWx4xTJ83T4xoCcVYQAvD_BwE

Software tool for data analysis from time stack chemotaxis experiments. Based on NIH ImageJ image processing system.

Proper citation: Chemotaxis and Migration Tool (RRID:SCR_022708) Copy   

•   Source: SciCrunch Registry

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://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