Tutorial

Here we provides comprehensive and step wise tutorials to analyse different datasets:

ChIPseq data analysis

RNAseq data analysis

Analysis Pipeline For 3’RNA-seq

Single Cell RNAseq data analysis

Proteomics/Mass Spectroscopy

Microarray data analysis

Gene co-expression network and Gene regulatory network

Visualizes data in a circular plots

Gene Set Enrichment Analysis (GSEA)

GWAS/ Variant Calling Pipeline

Machine Learning in Genomics

Bioinformatics Training Courses


ChIPseq data analysis

Practical Guidelines for the Comprehensive Analysis of ChIP-seq Data

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

ChIP-seq analysis notes from Tommy Tang

Q & A ChIP-seq technologies and the study of gene regulation

A survey of tools for variant analysis of next-generation genome sequencing data

CGAT: a model for immersive personalized training in computational genomics

NGS data analysis with R / Bioconductor: ChIP-Seq workflow

The Analysis of ChIP-Seq Data

EBI ChIP-seq analysis

Introduction to ChIP-Seq data and analysis

Hands-on introduction to ChIP-seq analysis – VIB Training

ENCODE: TF ChIP-seq pipeline

Pipeline for ChIP-seq preprocessing

A comprehensive comparison of tools for differential ChIP-seq analysis

Analysis of ChIP-seq data using Galaxy

ChIP-Seq data analysis ( Galaxy Training)


RNAseq data analysis

A survey of best practices for RNA-seq data analysis

RNA-seq workflow: gene-level exploratory analysis and DE

RNAseq analysis notes from Tommy Tang

 Informatics for RNA-seq: A web resource for analysis on the cloud

Analysis of RNA ‐ Seq Data

RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks.

EBI RNA-Seq exercise

An open RNA-Seq data analysis pipeline tutorial with an example

RNA-Seq Analysis Workflow

Transcript-level expression analysis of RNA-seq experiments

quanTIseq is a computational pipeline for the quantification of the Tumor Immune contexture from human RNA-seq data

quanTIseq documentation


Analysis Pipeline For 3’RNA-seq

QuantSeq 3′ mRNA sequencing for RNA quantification

Analysis of Lexogen Quantseq Data: Part 1


Single Cell RNAseq data analysis

Single Cell RNAseq data analysis Tutorial

A step-by-step workflow for low-level analysis of single-cell RNA-seq data

A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor

SCell: single-cell RNA-seq analysis software

https://github.com/diazlab/SCell

Seurat R package designed for QC, analysis, and exploration of single cell RNA-seq data

Getting Started with Seurat

Beta-Poisson model for single-cell RNA-seq data analyses

https://github.com/nghiavtr/BPSC

Sincera: A Computational Pipeline for Single Cell RNA-Seq Profiling Analysis

https://research.cchmc.org/pbge/sincera.html

SC3 – consensus clustering of single-cell RNA-Seq data

http://biorxiv.org/content/early/2016/09/02/036558

Citrus: A toolkit for single cell sequencing analysis

http://biorxiv.org/content/early/2016/09/14/045070

Single-Cell Resolution of Temporal Gene Expression during Heart Development

http://www.cell.com/developmental-cell/fulltext/S1534-5807(16)30682-7

Scalable latent-factor models applied to single-cell RNA-seq data separate biological drivers from confounding effects

http://biorxiv.org/content/early/2016/11/15/087775

Single cell transcriptomes identify human islet cell signatures and reveal cell-type-specific expression changes in type 2 diabetes

http://genome.cshlp.org/content/early/2016/11/18/gr.212720.116.abstract

SCODE: An efficient regulatory network inference algorithm from single-cell RNA-Seq during differentiation

http://biorxiv.org/content/early/2016/11/21/088856

SCOUP is a probabilistic model to analyze single-cell expression data during differentiation

https://github.com/hmatsu1226/SCOUP

scLVM is a modelling framework for single-cell RNA-seq data

https://github.com/PMBio/scLVM

Selective Locally linear Inference of Cellular Expression Relationships (SLICER) algorithm for inferring cell trajectories

https://github.com/jw156605/SLICER

SinQC: A Method and Tool to Control Single-cell RNA-seq Data Quality

http://www.morgridge.net/SinQC.html

TSCAN: Pseudo-time reconstruction and evaluation in single-cell RNA-seq analysis

https://github.com/zji90/TSCAN

Visualization and cellular hierarchy inference of single-cell data using SPADE

http://www.nature.com/nprot/journal/v11/n7/full/nprot.2016.066.html

OEFinder: Identify ordering effect genes in single cell RNA-seq data

https://github.com/lengning/OEFinder

SCANPY: large-scale single-cell gene expression data analysis

https://github.com/theislab/Scanpy


Proteomics/Mass Spectrometry/Data Analysis/ Interpretation


Microarray data analysis

Using Bioconductor for Microarray Analysis

An end to end workflow for differential gene expression using Affymetrix microarrays

A Tutorial Review of Microarray Data Analysis

Microarray analysis exercises 1 – with R

Analyze your own microarray data in R/Bioconductor

Analysing microarray data in BioConductor

Microarray Data Analysis

Processing Affymetrix Gene Expression Arrays

R package for Meta-Analysis of MicroArray

Key Issues in Conducting a Meta-Analysis of Gene Expression Microarray Datasets


Visualizes data in R

Circos Plot

Introduction to Circos plot ppt

RCircos: an R package for Circos 2D track plots

Package RCircos

OmicCircos

Circos Google Group

Network visualization with R

Useful link

circlize

Useful link

Useful link


Gene Set Enrichment Analysis (GSEA)

Introduction

reference paper

Pre-Ranked GSEA function

GSEAPY Example

fgsea: An R-package for fast preranked gene set enrichment analysis (GSEA)


Gene co-expression network and Gene regulatory network

GENIE3: GEne Network Inference with Ensemble of trees

https://bioconductor.org/packages/devel/bioc/vignettes/GENIE3/inst/doc/GENIE3.html

CoExpNetViz Comparative Co-Expression Network Construction and Visualization
http://bioinformatics.psb.ugent.be/webtools/coexpr/

GeneNetworkBuilder Guide: Build Regulatory Network from ChIP-chip/ChIP-seq and Expression Data
https://bioconductor.org/packages/release/bioc/vignettes/GeneNetworkBuilder/inst/doc/GeneNetworkBuilder_vignettes.html

CoRegNet: Reconstruction and integrated analysis of Co-Regulatory Networks
https://bioconductor.org/packages/release/bioc/vignettes/CoRegNet/inst/doc/CoRegNet.html

ARACNE: An Algorithm for the Reconstruction of Gene Regulatory Networks

http://califano.c2b2.columbia.edu/aracne/

ARACNe-inferred gene networks from TCGA tumor datasets
https://bioconductor.org/packages/release/data/experiment/html/aracne.networks.html

WGCNA: an R package for weighted correlation network analysis

https://labs.genetics.ucla.edu/horvath/CoexpressionNetwork/Rpackages/WGCNA/

MERLIN: An approach to capture per-gene and per-module regulatory information

http://pages.discovery.wisc.edu/~sroy/merlin/index.html

coexnet: An R package to build CO-EXpression NETworks from Microarray Data

https://www.bioconductor.org/packages/3.7/bioc/vignettes/coexnet/inst/doc/coexnet.pdf

RTN: reconstruction of transcriptional networks and analysis of master regulators.

http://bioconductor.org/packages/devel/bioc/vignettes/RTN/inst/doc/RTN.html


GWAS/ Variant Calling Pipeline

Genome-Wide Association Studies

Variant Calling Pipeline: FastQ to Annotated SNPs in Hours

A simple SNP calling pipeline

Hands-on Tutorial on SNP Calling

Genome Analysis Toolkit


Machine learning in Genomics

Machine learning applications in  genetics and genomics

Deep learning, genomics, and precision medicine

Deep Learning for Cancer Immunotherapy


Bioinformatics Training Courses

Cancer Research UK Cambridge Bioinformatics core facility

HarvardX Biomedical Data Science Open Online Training

SIB Virtual Computational Biology Seminar Series

Training Courses by the Babraham Institute the Bioinformatics group

JCBioinformatics

Bioinformatics Crash Course

Next-Gen Sequence Analysis Workshop (2013)

R and NGS tutorial

Bioinformatics Resources by Obi Griffith

Tutorials developed and maintained by the worldwide Galaxy community