Links Úteis

Sequenciamento de Nova Geração (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

Bioinformática aplicada a oncologia:

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

Análise de transcriptoma (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 

Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments 

Challenges and strategies in transcriptome assembly and differential gene expression quantification. A comprehensive in silico assessment of RNA-seq experiments 

Statistical design and analysis of RNA sequencing data 

A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae

A survey of best practices for RNA-seq data analysis

A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing 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

A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium

An useful post: Review papers on the topic of RNA-seq

Enriquecimento de vias e redes:

How to visually interpret biological data using networks

Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles

Identificação de variantes no genoma:

Genome structural variation discovery and genotyping

Genotype and SNP calling from next-generation sequencing data

Análises de sobrevida: o que você precisa saber?

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 III: Multivariate data analysis – choosing a model and assessing its adequacy and fit

Survival Analysis Part IV: Further concepts and methods in survival analysis

Cursos Online:

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 

RNA-seq Bioinformatics

Bioinformatics Training Courses - Instituto Gulbenkian de Ciência 

[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

Tutoriais:

Rosalind - Aprenda bioinformática online através de problemas!

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

RNA-seqlopedia

RNA-Seq De novo Assembly Using Trinity

RNA-seq workflow: gene-level exploratory analysis and differential expression

ENCODE RNA-Seq Standards

RNA-seq tutorials | RNA-seq Lectures 

The Ultimate Guide To Partitioning Clustering 

GNU/Linux:

Practical Introduction to Linux

Unix Bootcamp

UNIX Tutorial for Beginners

The Unix Shell lesson from The Carpentries

Introduction to HPC

R:

Introduction to R

Quick & Dirty Guide to R 

R Tutorial – Learn R programming language

Cookbook for 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 

Survival Analysis in R

TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages

Introduction to DGE

Programas úteis / 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