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Bioinformatics Data Analysis Pipeline- Spatial Transcriptomics

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Bioinformatics Data Analysis Pipeline- Spatial Transcriptomics

  • Space Ranger

    Space Ranger is a set of analysis pipelines that process 10x Genomics Visium data with brightfield or fluorescence microscope images, allowing users to map the whole transcriptome in a variety of tissues. Space Ranger v3.0 now supports Visium HD.

    Reference: PMID: 28091601

    Contact: Qin Ma

  • BayesSpace

    A fully Bayesian statistical method that uses the information from spatial neighborhoods for resolution enhancement of spatial transcriptomic data and for clustering analysis.

    Reference: PMID: 34083791

    Contact: Qin Ma

  • SPRUCE

    A Bayesian spatial multivariate finite mixture model based on multivariate skew-normal distributions, which is capable of identifying distinct cellular sub-populations in HST data.

    Reference: PMID: 35895854

    Contact: Qin Ma

  • SpaGCN

    A graph convolutional network approach that integrates gene expression, spatial location and histology in SRT data analysis. Through graph convolution, SpaGCN aggregates gene expression of each spot from its neighboring spots, which enables the identification of spatial domains with coherent expression and histology. 

    Reference: PMID: 34711970

    Contact: Qin Ma

  • SPARK-X

    A non-parametric method for rapid and effective detection of spatially expressed genes in large spatial transcriptomic studies.

    Reference: PMID: 34154649

    Contact: Qin Ma

  • RCTD

    A computational method that leverages cell type profiles learned from single-cell RNA-seq to decompose cell type mixtures in spatial transcriptomic while correcting for differences across sequencing technologies.

    Reference: PMID: 33603203

    Contact: Qin Ma

  • CARD

    A deconvolution method that combines cell-type-specific expression information from single-cell RNA sequencing (scRNA-seq) with correlation in cell-type composition across tissue locations.

    Reference: PMID: 35501392

    Contact: Qin Ma

  • SpaTalk

    A graph network and knowledge graph to model and score the ligand-receptor-target signaling network between spatially proximal cells by dissecting cell-type composition through a non-negative linear model and spatial mapping between single-cell transcriptomic and spatially resolved transcriptomic data.

    Reference: PMID: 35908020

    Contact: Qin Ma

  • COMMOT

    It can infer cell–cell communication in spatial transcriptomics, which accounts for the competition between different ligand and receptor species as well as spatial distances between cells.

    Reference: PMID: 36690742

    Contact: Qin Ma

Bioinformatics Data Analysis Pipeline- Single Cell RNA-Seq

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Bioinformatics Data Analysis Pipeline- Single Cell RNA-Seq

  • Cell Ranger

    A set of analysis pipelines that perform sample demultiplexing, barcode processing, single cell 3' and 5' gene counting, V(D)J transcript sequence assembly and annotation and Feature Barcode analysis from single cell data.

    Reference: PMID: 28091601

    Contact: Qin Ma

  • Seurat

    Seurat is an R package designed for QC, analysis, and exploration of single-cell RNA-seq data. Seurat aims to enable users to identify and interpret sources of heterogeneity from single-cell transcriptomic measurements and to integrate diverse types of single-cell data.

    Reference: PMID: 37231261

    Contact: Qin Ma

  • Monocole3

    An unsupervised algorithm to infer transcriptome dynamics of a temporal process such as cell differentiation using single-cell RNA-Seq data.

    Reference: PMID: 24658644

    Contact: Qin Ma

  • Slingshot

    A method for inferring cell lineages and pseudotimes from single-cell gene expression data.

    Reference: PMID: 29914354

    Contact: Qin Ma

  • SingleR

    A computational framework for the annotation of scRNA-seq by reference to bulk transcriptomes.

    Reference: PMID: 30643263

    Contact: Qin Ma

  • ScType

    A fully-automated and ultra-fast cell-type identification based solely on a given scRNA-seq data, along with a comprehensive cell marker database as background information.

    Reference: PMID: 35273156

    Contact: Qin Ma

  • Azimuth

    A web application that uses an annotated reference dataset to automate the processing, analysis and interpretation of a new single-cell RNA-seq or ATAC-seq experiment.

    Reference: PMID: 31178118

    Contact: Qin Ma

  • Scanpy

    A scalable toolkit for analyzing single-cell gene expression data.  It includes preprocessing, visualization, clustering, trajectory inference and differential expression testing.

    Reference: PMID: 29409532

    Contact: Qin Ma

  • Harmony

    An algorithm that projects cells into a shared embedding in which cells group by cell type rather than dataset-specific conditions.

    Reference: PMID: 31740819

    Contact: Qin Ma

  • MAGIC

    A method that shares information across similar cells, via data diffusion, to denoise the cell count matrix and fill in missing transcripts.

    Reference: PMID: 29961576

    Contact: Qin Ma

  • CellChat

    A tool that is able to quantitatively infer and analyze intercellular communication networks from single-cell RNA-sequencing (scRNA-seq) data

    Reference: PMID: 33597522

    Contact: Qin Ma

  • IRIS3

    A web server for active regulons within a specific cell type, i.e., cell-type-specific regulons (CTSR), inference from scRNA-Seq data for human and mouse

    Reference: PMID: 32421805

    Contact: Qin Ma

  • ScGNN

    scGNN (single-cell graph neural network) can provide a hypothesis-free deep learning framework for scRNA-Seq analyses. scGNN provides an effective representation of gene expression and cell–cell relationships. It is also a powerful framework that can be applied to general scRNA-Seq analyses.

    Reference: PMID: 33767197

    Contact: Qin Ma

Bioinformatics Data Analysis Pipeline- TCR-Seq

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Bioinformatics Data Analysis Pipeline- TCR-Seq

Bioinformatics Data Analysis Pipeline- Genetic Variant Analysis

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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

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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

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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

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