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Bioinformatics Data Analysis Pipeline- TCR-Seq

Data being organized

Bioinformatics Data Analysis Pipeline- TCR-Seq

Bioinformatics Data Analysis Pipeline- Genetic Variant Analysis

Data being organized

Bioinformatics Data Analysis Pipeline- Genetic Variant Analysis

  • GATK

    Genome Analysis Toolkit Best Practices Pipeline

    Reference: PMID: 25431634

    Contact: Qin Ma

  • VarScan

    Tool for detecting SNPs,indels, somatic mutations and copy number variants in exome data.

    Reference: PMID: 22300766

    Contact: Qin Ma

  • HaplotypeCaller

    Tool under GATK to call germline SNPs and indels via local re-assembly of haplotypes.

    Reference: https://www.biorxiv.org/content/10.1101/201178v3

    Contact: Qin Ma

  • Mutect

    Tool under GATK  to call somatic SNVs and indels via local assembly of haplotypes.

    Reference: PMID: 20644199

    Contact: Qin Ma

  • CNVKit

    Genome wide copy number detection and visualization from targeted DNA sequencing.

    Reference: PMID: 27100738

    Contact: Qin Ma

  • VEP

    Variant Effect Predictor to annotate variants using Ensembl.

    Reference: PMID: 27268795

    Contact: Qin Ma

  • VCFtools

    A package designed to access methods to manage complex genetic variation in form of vcf format.

    Reference: PMID: 21653522

    Contact: Qin Ma

  • Picard

    A set of command line tools for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.

    Reference: https://broadinstitute.github.io/picard/

    Contact: Qin Ma

Bioinformatics Data Analysis Pipeline- Methylation

Data being organized

Bioinformatics Data Analysis Pipeline- Methylation

  • Bismark

    A tool to map bisulfite converted sequence reads and determine cytosine methylation states.

    Reference: PMID: 21493656

    Contact: Qin Ma

  • TrimGalore

    A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data.

    Contact: Qin Ma

  • DSS

    An R library performing differntial analysis for count-based sequencing data. It detectes differentially expressed genes (DEGs) from RNA-seq, and differentially methylated loci or regions (DML/DMRs) from bisulfite sequencing (BS-seq)

    Reference: PMID: 23001152

    Contact: Qin Ma

  • MethylKit

    R package for DNA methylation analysis and annotation from high-throughput bisulfite sequencing. 

    Reference: PMID: 23034086

    Contact: Qin Ma

Bioinformatics Data Analysis Pipeline- ChIP-Seq

Data being organized

Bioinformatics Data Analysis Pipeline- ChIP-Seq

  • DeepTools

    Tools for exploring deep sequencing data especially ChIPseq.

    Reference: PMID: 27079975

    Contact: Qin Ma

  • MACS2

    Transcription factor peak caller for CHIPseq and any other type of DNA enrichment.

    Reference: PMID: 18798982

    Contact: Qin Ma

  • ChIPpeakAnno

    Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments, or any experiments that result in large number of genomic interval data.

    Reference: PMID: 20459804

    Contact: Qin Ma

  • DiffBind

    Differential Binding Analysis of ChIP-Seq Peak Data.

    Reference: PMID: 25972895

    Contact: Qin Ma

  • HOMER

    Software for motif discovery and next-gen sequencing analysis.

    Reference: PMID: 20513432

    Contact: Qin Ma

Bioinformatics Data Analysis Pipeline- RNA-Seq

Data being organized

Bioinformatics Data Analysis Pipeline- RNA-Seq

  • EdgeR

    Differential expression analysis using bulk RNA-seq data

    Reference: PMID: 19910308

    Contact: Qin Ma

  • DESeq2

    Differential expression analysis using bulk RNA-seq data.

    Reference: PMID: 25516281

    Contact: Qin Ma

  • Limma

    Differential expression analysis using bulk RNA-seq and microarray data.

    Reference: PMID: 25605792

    Contact: Qin Ma

  • RSeQC

    RNAseq quality control package.

    Reference: PMID:22743226

    Contact: Qin Ma

  • JunctionSeq

    Bioconductor package for detection and visualization of differential usage of exons and splice junctions in High-Throughput, Next-Generation RNA-Seq datasets.

    Reference: PMID: 27257077

    Contact: Qin Ma

  • CIBERSORT

    A deconvolution-based method thats estimates each immune cell type's relative proportion from a gene expression profile (GEP).

    Reference: PMID: 29344893

    Contact: Qin Ma

Bioinformatics Data Analysis Pipeline- General Tools

Data being organized

Bioinformatics Data Analysis Pipeline- General Tools

  • Bowtie2

    Ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences,

    Reference: PMID: 22388286

    Contact: Qin Ma

  • LEfSe

    Determines the features (organisms, clades, operational taxonomic units, genes or functions) most likely to explain differences between classes by coupling standard tests for statistical significance with additional tests encoding biological consistency and effect relevance.

    Reference: PMID: 21702898

    Contact: Qin Ma

  • FastQC

    A quality control tool for high throughput sequence data.

    Reference: PMID: 21702898

    Contact: Qin Ma

  • Samtools

    Reading/writing/editing/indexing/viewing SAM/BAM/CRAM format.

    Reference: PMID: 33590861

    Contact: Qin Ma

  • HISAT2

    HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes as well as to a single reference genome.

    Reference: PMID: 25751142

    Contact: Qin Ma

  • Bwa

    Software package for mapping DNA sequences against a large reference genome.

    Reference: PMID: 19451168

    Contact: Qin Ma

  • Bedtools

    Versatile command line toolkit to analyze genomic features.

    Reference: PMID:20110278

    Contact: Qin Ma

  • Featurecounts

    An efficient general purpose program for assigning sequence reads to genomic features.

    Reference: PMID: 24227677

    Contact: Qin Ma

  • Cutadapt

    Tool used for adapter trimming.

    Reference: https://doi.org/10.14806/ej.17.1.200

    Contact: Qin Ma

  • Integrative Genomics Viewer

    Viewer for sequence alignment data.

    Reference: PMID: 21221095

    Contact: Qin Ma

  • Nf-Core

    A community effort to collect a curated set of analysis pipelines built using Nextflow.

    Reference: PMID: 32055031

    Contact: Qin Ma

Bioinformatics Data Analysis Pipeline

Data being organized

Bioinformatics Data Analysis Pipeline

These resources are divided by the following categories: General Tools, RNA-Seq, ChIP-Seq, Methylation, Genetic Variant Analysis, TCR-Seq, Single Cell RNA-Seq, Spatial Transcriptomics, Other Bioinformatics Analyses, Pathway Analysis and Omics Experimental Design.

Bioinformatics Data Analysis Pipeline Resources

General Tools

General Tools

RNA-Seq

RNA-Seq

ChIP-Seq

ChIP-Seq

Methylation

Methylation

Genetic Variant Analysis

Genetic Variant Analysis

TCR-Seq

TCR-Seq

Single Cell RNA-Seq

Single Cell RNA-Seq

Spatial Transcriptomics

Spatial Transcriptomics

Pathway Analysis

Pathway Analysis

Omics Experimental Design

Omics Experimental Design

Other Bioinformatics Analyses

Other Bioinformatics Analyses

Generative AI

Person using AI assistant

Generative AI

  • GPT-4

    GPT-4 can generate, edit and iterate with users on creative and technical writing tasks, such as composing songs, writing screenplays or learning a user’s writing style.

    Contact: Ping Zhang

  • Gemini

    Gemini is a large language model that can generate text, translate languages, write different kinds of creative content, and answer your questions in an informative way. It is trained on a massive amount of text data, which allows it to communicate and generate human-like text in response to a wide range of prompts and questions.

    Contact: Ping Zhang

  • Llama 3

    The open source AI model, by Meta, you can fine-tune, distill and deploy anywhere.

    Contact: Ping Zhang

AI for Drug Development

Doctor holding graphic of AI

AI for Drug Development

  • Modof

    Modof is a generative AI tool for lead optimization. Given a lead to optimize and its desired properties, Modof intelligently changes a few fragments of the lead molecule and modifies the lead into another similar molecule which has better desired properties. Modof generates such optimized molecules automatically without expert knowledge input. 

    Referece: PMID:35187404

    Contact: Xia Ning

  • G2Retro

    G2retro is a generative AI tool to generate one-step synthesis routes for any given product. It can produce multiple possible synthesis routes that are feasible and can vary. G2retro generates such routes without expert knowledge input. 

    Reference: PMID: 37253928

    Contact: Xia Ning

  • TCRPPO

    TCRPPO is a generative AI tool for peptide design. It generates T-cell receptors (TCRs) that can better recognize given peptides. 

    Reference: https://link.springer.com/chapter/10.1007/978-3-031-29119-7_11

    Contact: Xia Ning

  • LlaSMol

    LlaSMol is a Large-Lanauge Model (LLM) together with a high-quality instruction tuning dataset for a wide variety of tasks in drug development, including property prediction, forward synthesis, name convension, etc. 

    Reference: to appear in COLM 2024

    Contact: Xia Ning

  • DeepCE

    Deep learning framework for high-throughput mechanism-driven phenotype compound screening

    Reference: PMID: 33796820

    Contact: Ping Zhang

  • CIGER

    Chemical-induced gene expression ranking.

    Reference: PMID: 35465231

    Contact: Ping Zhang

Graduate Students in Biomedical, Clinical and Translational Research Seminar Series

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