Do you want to know more about some of the softwares we use? Are you unsure about how to work with your data? You will find below some tutorials, courses and links that can help you with your research.
Next Generation Sequencing (NGS):
Coming of age: ten years of next-generation sequencing technologies
Nature Series: Applications of next-generation sequencing
Next-generation genomics: an integrative approach
Sequencing technologies — the next generation
A survey of sequence alignment algorithms for next-generation sequencing
Bioinformatics applied to oncology:
Computational genomics tools for dissecting tumour–immune cell interactions
Expanding the computational toolbox for mining cancer genomes
Functional variomics and network perturbation: connecting genotype to phenotype in cancer
Nature Collection: Cancer genomics — from bench to bedside
Transcriptome analysis (RNA-Seq):
RNA sequencing: advances, challenges and opportunities
A comparison of methods for differential expression analysis of RNA-seq data
Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples
Statistical design and analysis of RNA sequencing data
A survey of best practices for RNA-seq data analysis
Near-optimal RNA-Seq quantification
Differential analyses for RNA-seq- transcript-level estimates improve gene-level inferences
Informatics for RNA Sequencing: A Web Resource for Analysis on the Cloud
Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown
Methods to study splicing from high-throughput RNA sequencing data
An useful post: Review papers on the topic of RNA-seq
Networks and Pathway Enrichment:
How to visually interpret biological data using networks
Identification of genome variants:
Genome structural variation discovery and genotyping
Genotype and SNP calling from next-generation sequencing data
Survival Analysis: what do you need to know?
Survival Analysis Part I: Basic concepts and first analyses
Survival Analysis Part II: Multivariate data analysis – an introduction to concepts and methods
Survival Analysis Part IV: Further concepts and methods in survival analysis
Online courses:
Bioinformatics: Introduction and Methods
Bioinformatic Methods I 'Next Gen' Sequence Analysis (RNA-Seq) / Metagenomics
Command Line Tools for Genomic Data Science
Data Analysis for Life Sciences 7: Case Studies in Functional Genomics
Differential gene expression workshop
Genome Sequencing (Bioinformatics II)
Introduction to Genomic Technologies
Bioinformatics for Cancer Genomics
[Papers-technical related]
A Quick Guide to Organizing Computational Biology Projects
An Online Bioinformatics Curriculum
A Quick Introduction to Version Control with Git and GitHub
Tutorials:
Rosalind - Aprenda bioinformática online através de problemas!
Informatics for RNA-seq: A web resource for analysis on the cloud
RNA-Seq De novo Assembly Using Trinity
RNA-seq workflow: gene-level exploratory analysis and differential expression
RNA-seq tutorials | RNA-seq Lectures
The Ultimate Guide To Partitioning Clustering
GNU/Linux:
Practical Introduction to Linux
R:
Elegant correlation table using xtable R package
ggfortify : Extension to ggplot2 to handle some popular packages - R software and data visualization
ggbio - Visualize genomic data
Gviz - Plotting data and annotation information along genomic coordinates
ReportingTools - Tools for making reports in various formats
Interactive Network Visualization using R
Practical Guide to Principal Component Methods in R
TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages
Useful Software / Pipelines:
Cancer Cell Metabolism Gene DB - Online tool
jvenn - Online venn diagram creator
MultiQC - Aggregate results from bioinformatics analyses across many samples into a single report
RNACocktail - A comprehensive framework for accurate and efficient RNA-Seq analysis