Clinical and Translational Science Institute
Advancing today’s discoveries to improve health for all.

Tools of the Trade: Clinical Research Resources from the Clinical and Translational Science Institute

Annual Scientific Meeting

SoCRA Certification Exam

RAPTIC Learning Session

Neuroscience Research Institute 2nd Annual Translational Short Course

Clinical and Translational Science Research Program Proposal Ideation Workshop

Clinical and Translational Science Research Program Information Session

Bioinformatics Data Analysis Pipeline- Omics Experimental Design

Data being organized

Bioinformatics Data Analysis Pipeline- Omics Experimental Design

  • POWSC

    A simulation-based method, to provide power evaluation and sample size recommendation for single-cell RNA-sequencing DE analysis.

    Reference: PMID: 32614380

    Contact: Qin Ma

  • SCOPIT

    A sample size calculator for single-cell sequencing experiments regarding cell subpopulation identification.

    Reference: PMID: 31718533

    Contact: Qin Ma

  • RNASeqPower

    Power analysis for bulk RNA-seq data.

    Reference: PMID: 23961961

    Contact: Qin Ma

  • ssizeRNA

    Power analysis for bulk RNA-seq data.

    Reference: PMID: 27029470

    Contact: Qin Ma

Bioinformatics Data Analysis Pipeline- Pathway Analysis

Data being organized

Bioinformatics Data Analysis Pipeline- Pathway Analysis

  • IPA

    Visualize complex ‘omics data, perform insightful data analysis and interpret your experimental results in the context of biological systems.

    Reference: PMID: 24336805

    Contact: Qin Ma

  • clusterProfiler

    R Package for Comparing Biological Themes Among Gene Clusters

    Reference: PMID: 22455463

    Contact: Qin Ma

  • Gene Set Enrichment Analysis

    A computational method that determines whether an a priori defined set of genes shows statistically significant, concordant differences between two biological states.

    Reference: PMID: 16199517

    Contact: Qin Ma

Bioinformatics Data Analysis Pipeline- Other Bioinformatics Analyses

Data being organized

Bioinformatics Data Analysis Pipeline- Other Bioinformatics Analyses

  • miRDeep2

    Discovers active known or novel miRNAs from deep sequencing data.

    Reference: PMID: 21911355

    Contact: Qin Ma

  • Juicer

    A platform for analyzing kilobase resolution Hi-C data. In this distribution, we include the pipeline for generating Hi-C maps from fastq raw data files and command line tools for feature annotation on the Hi-C maps.

    Reference: PMID: 27467249

    Contact: Qin Ma

  • QIIME2

    Next-generation microbiome bioinformatics platform that is extensible, free and open source.

    Reference: PMID: 32343490

    Contact: Qin Ma

  • Transcriptome Analysis Console

    QC, normalization, and differential expression of affymetrix microarray data.

    Contact: Qin Ma

  • XCMS

    An R package which provides a framework for processing LC/MS spectral data.

    Reference: PMID: 16448051

    Contact: Qin Ma

  • CAMERA

    An R package which provides collection of annotation related methods for mass spectrometry data.

    Reference: PMID: 22111785

    Contact: Qin Ma

  • Parse Biosciences Pipeline

    Data analysis software package for Parse data.

    Contact: Qin Ma

     

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