Curator Dashboard

Software R package for DNA copy number detection from off-target sequence data. Used to extract DNA copy number information from targeted sequencing by utiizing off-target reads.

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• RRID
• 2 years ago - by Anonymous

Web tool for protein structure prediction, leveraging sequence alignment, template-based modeling, deep learning, and validation techniques. With input of either amino acid sequence or FASTA file, ProStruc generates protein structures. ProStruc automates process of blast searches, template selection, structural modeling, and validation, including RMSD, TM-score, and QMEAN.

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• 2 years ago - by Anonymous

Core assists investigators to identify and quantify proteins and their modifications that are differentially expressed in cells, tissues or body fluids, to track interactions with binding partners during changes in signal transduction, and to identify proteolytic cleavage sites and map post-translational modifications by providing following proteomic services: Consultation, Sample preparation,Protein Identification,Protein Modifications, Protein Quantification, Targeted Quantification, High Resolution Mass Analysis,Training and Self-Service Equipment. Core offers workshops to use the Core’s MALDI-TOF mass spectrometer, Typhoon gel imaging scanner and 2D gel electrophoresis equipment and proteomic software.

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• 2 years ago - by Anonymous

Portal provides access to data set including, for each U.S. census tract (defined using 2010 census tract boundaries), certain social determinants of health data elements, including race/ethnicity, education, poverty, urban/rural, socioeconomic status, and racial residential segregation indices defined using 2008-2012 American Community Survey data and 2010 definitions of rural urban commuting areas.

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• 2 years ago - by Anonymous

Core offers services related to cryo electron microscopy. Services include grid preparation, screening and data collection, as well as user training.

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• SciCrunch
• 2 years ago - submitted by Edyta Vieth

BIDMC Bioinformatics Core is Unit of the Precision RNA Medicine Core and provides support for management, integration and contextual analysis of biological high-throughput data, training on tools, databases and best practice.

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• SciCrunch
• 2 years ago - submitted by Edyta Vieth

Collaborative open project of Chan Zuckerberg Initiative and Chan Zuckerberg Biohub. The no-code, cloud-based bioinformatics tool for researchers. Used to analyzing genomic data for free. Hypothesis-free global software platform that helps scientists identify pathogens in metagenomic sequencing data.

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• 2 years ago - submitted by Anita Bandrowski

Benchtop pH Meter to record accurate and reliable pH, mV, ORP and temperature measurements.

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• 2 years ago - submitted by Brianna Miller

Real-time PCR system that enables precise quantitative real-time PCR results. High-quality qPCR results, 4-color, 96-well PCR instrument.

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• 2 years ago - by Anonymous

Software tool for gene fusion detection from RNA-Seq data. Fusion detection algorithm specifically designed to meet demanding requirements of HTS-assisted precision oncology. Capable of detecting aberrant transcripts that are not called by most fusion detection methods but may be clinically relevant. This includes tumor suppressor genes that are occasionally inactivated by rearrangements within the gene or by translocations to introns or intergenic regions.

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• 2 years ago - by Anonymous

Software tool to leverage chimeric and discordant read alignments identified by STAR aligner to predict fusions. Component of Trinity Cancer Transcriptome Analysis Toolkit. Used to identify candidate fusion transcripts supported by Illumina reads. Maps junction reads and spanning reads to reference annotation set.

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• RRID
• 2 years ago - by Anonymous

Core provides multidimensional LC-MS/MS analysis including Protein ID, Proteomics Profiling, Targeted Proteomics and Post Translational Modification analysis. Quantitative proteomic services are provided using label free quantitative proteomic (LFQ) profiling, Tandem mass tagging (TMT) or SILAC approaches. Provides support for macromolecular complexes using Nano ESI.

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• 2 years ago - by Anonymous

Software tool for fast and accurate alignment of BS-Seq reads using bwa-mem and 3-letter genome.

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• 2 years ago - by Anonymous

Software tool to process coordinate sorted and indexed BAM or CRAM file containing some form of BS-seq alignments and extract per-base methylation metrics from them. MethylDackel requires indexed fasta file containing reference genome as well.

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• 2 years ago - by Anonymous

Software R package as whole genome DNA methylation analysis pipeline. Used for testing differentially methylated cytosines or regions in whole-genome bisulfite sequencing or reduced representation bisulfite sequencing experiments. Several options exist for either site-specific or sliding window tests, and variance estimation.

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• 2 years ago - by Anonymous

Software analysis pipeline that process 10x Genomics Visium data with brightfield or fluorescence microscope images, allowing users to map whole transcriptome in variety of tissues.

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• 2 years ago - by Anonymous

Desktop application for Windows and MacOS that allows to interactively visualize data generated by the Xenium Analyzer instrument.

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• RRID
• 2 years ago - by Anonymous

Cell counting chamber. Used to count cells or other particles in suspensions under microscope.

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• RRID
• 2 years ago - by Anonymous

Software tool to assist in optimizing nucleotide pooling strategies for high-throughput genomic analyses. Used to evaluate nucleotide distribution uniformity across positions and allows users to set customizable red flag thresholds, ensuring optimal results while accommodating variability.

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• RRID
• 2 years ago - by Anonymous

Core specializes in analysis of nascent transcriptome using PRO-seq and TT-seq NGS methods. Provides services allowing users to submit prepared cells and receive analyzed data. Offers free consultations to help with experimental design, answer questions, and discuss data analysis.

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• RRID
• 2 years ago - by Anonymous