Curator Dashboard

Core covers main techniques of electron microscopy, from scanning electron microscopy to scanning transmission electron microscopy, for characterization of morphology and structure of materials at micrometer and nanometer scale.Provides equipment for preparing samples for analysis by different electron microscopy techniques.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software tool for high resolved spatial transcriptomics. Smoothing approach for spatial transcriptome data with ultrahigh resolution. Used to determine neighborhood relationship of cells, to calculate smoothing contribution to recalculate the gene expression of each cell.

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• RRID
• 3 years ago - submitted by Tongxuan Lv

Core offers flow cytometry analysis and cell sorting services. It houses FACS Aria II 5-laser, 14-color sorter, SH800 2-laser, 6-color user-run cell sorter, COPAS Select, Drosophila embryo and large particle sorter, LSRII, 4-laser, 14-color analyzer, MACSQuant VYB 3-laser, 8-color analyzer with 96-well plate option, as well as Moxi Z cell counter technology used for determining cell concentration and size distribution and Miltenyi QuadroMACS separator. Services include technician assisted sorting, as well as training for analyzers, SH800 and Moxi instruments. Help with experimental design is available.Facility maintains workstation with flow cytometry data analysis software, and has copy of this software as well as site license for use outside of facility.

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• RRID
• 3 years ago - by Anonymous

Software R package for comprehensive analysis chromatin accessibility data. Analyzing chromatin accessibility data in R. Used for data quality control, exploratory analyses including unsupervised methods for dimension reduction, clustering and quantifying transcription factor activities, and identification and characterization of differentially accessible regions. Used for analysis of large bulk datasets comprising hundreds of samples as well as for single cell datasets.

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• RRID
• 3 years ago - by Anonymous

Code to program and run flicker stimulation on BrainWAVE stimulator device. This brain oscillation stimulating software can be adapted across subjects and integrated into variety of experimental designs like electrophysiology, neuroimaging, EEG, MRI. Flexible method for noninvasive stimulation of brain rhythms across species. Used to measure effects of rhythmic brain activity on behavior.

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• RRID
• 3 years ago - submitted by Kevin Chavez Lopez

Software imputation model for scRNA-seq data. Used to accurately and efficiently identify dropout values and impute them precisely, which helps to improve downstream analyses of single-cell RNA sequencing data.

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• RRID
• 3 years ago - by Anonymous

Software toolkit for PET and SPECT. Simulation platform for medical imaging and radiotherapy. Used for modelling of planar scintigraphy, single photon emission computed tomography (SPECT) and positron emission tomography (PET) acquisitions, this platform is widely used to assist PET and SPECT research. Extension of this platform, released by OpenGATE collaboration as GATE V6, enables modelling of x-ray computed tomography and radiation therapy experiments.

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• RRID
• 3 years ago - by Anonymous

Galileo computer assisted Tissue Microarray instrument allows TMA preparation with different paraffin block sizes, producing digital excel format reporting and possibility of data transfer to several Digital TMA Slide Scanners for complete tracking of Tissue Microarray process.

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• RRID
• 3 years ago - by Anonymous

Software tool for tensiometry measurements and contact angle hysteresis.

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• RRID
• 3 years ago - by Anonymous

Software pipeline management system, written in Python. Enables reproducible, open source, big biomedical data analyses.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software tool for protein structure alignment based on TM-score.Used to identify structural alignment between protein pairs that combines the TM-score rotation matrix and Dynamic Programming. Used for sequence independent protein structure comparisons.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software tool for Himar1 TnSeq analysis.Provides graphical interface to three different statistical methods for analyzing TnSeq data. Used for identifying essential genes in individual datasets as well as comparative analysis between conditions.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software suite of tools for identification of modified nucleotides from nanopore sequencing data.Used also for analysis and visualization of raw nanopore signal.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software package written in Java for analysis of high-throughput sequencing data of transposon mutant libraries.Reads the alignment and the gene annotation, and provides the user with set of tools to investigate data and identify possibly essential or advantageous genes as those that contain significantly low counts of transposon insertions.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software tool to process raw sequenceing chromatograph trace files from EST projects into quality checked sequences, ready for submission to dbEST.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software tool for membrane protein structure prediction.Transmembrane topology prediction.Used for predicting topology of bacterial inner membrane proteins.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software toolkit for carrying out genetic association for multi-catagory phenotypes. Implements multinomial and ordinal association incorporating covariates, conditional analysis, empirical and non-emperical priors and fine-mapping.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software tool as post-processor for TopHat unmapped reads that restores read information in the proper format.Enables downstream software to process plethora of BAM files written by TopHat.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software tool to reconstruct phylogenetic trees from molecular sequence data by maximum likelihood. Allows analysis of large data sets and automatically assigns estimations of support to each internal branch. Computes pairwise maximum likelihood distances as well as branch lengths for user specified trees.Conducts statistical tests on the data set.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software tools for estimating expression in RNA-Seq data which performs sequencing of end tags of transcript, and incorporate molecular tags to correct for amplification bias.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth