Article Archive

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GRASS for Rapid Reannotation of RNAseq Data

  • annotation
  • graph

Zipper plot for visualizing transcriptional activity of genomic regions

  • visualization

SuperTranscript - a reference for analysis and visualization of the transcriptome

  • visualization

Lior Pachter's Zika Paper

  • kallisto
  • sleuth

Trimming of sequence reads alters RNA-Seq gene expression estimates

A survey of best practices for RNA-seq data analysis

RapMap - Today's Must Read Paper

An opinionated guide to the proper care and feeding of your transcriptome

Benchmark analysis of algorithms for determining and quantifying full-length mRNA splice forms from RNA-seq data

An opinionated guide to the proper care and feeding of your transcriptome

tximport: import and summarize transcript-level estimates for gene-level analysis

Timecourse analysis with Sleuth

TransRate: Reference Free Quality Assessment of de-novo Transcriptome Assemblies

Getting the Most Out of RNA-seq Data Analysis

Large-Scale Search of Transcriptomic Read Sets with Sequence Bloom Trees

Rail-RNA: Scalable analysis of RNA-seq splicing and coverage

Optimizing error correction of RNAseq reads

Pachter's Kallisto Comes with Unconventional License

Pachter Blogs on Sailfish vs Kallisto

Evaluation of tools for differential gene expression analysis by RNA-seq on a 48 biological replicate experiment

Kallisto from Pachterlab for RNAseq Quantification

Why Weight? Modelling Sample and Observational Level Variability Improves Power in RNA-seq Analyses

SplAdder: Identification, quantification and testing of alternative splicing events from RNA-Seq data

Large-Scale Search of Transcriptomic Read Sets with Sequence Bloom Trees

Do count-based differential expression methods perform poorly when genes are expressed in only one condition?

Utilizing de Bruijn graph of metagenome assembly for metatranscriptome analysis

Low-cost, low-input RNA-seq protocols perform nearly as well as high-input protocols

StringTie - A New Alignment + Assembly Based Method for RNAseq

Bridger: a new framework for de novo transcriptome assembly using RNA-seq data

Evaluation of de novo transcriptome assemblies from RNA-Seq data

Comparisons of computational methods for differential alternative splicing detection using RNA-seq in plant systems

HISAT: Hierarchical Indexing for Spliced Alignment of Transcripts

RNA-seq Data Analysis Course Materials

Chimeras and Fusion Transcripts in RNAseq Assembly

RNAseq: Does it Really Matter How You Analyze the Data?

SUPPA: a super-fast pipeline for alternative splicing analysis from RNA-Seq

High-Resolution Transcriptome Analysis with Long-Read RNA Sequencing

Influence of RNA Extraction Methods and Library Selection Schemes on RNA-seq Data

Benchmark Analysis of RNA-Seq is an Excellent Confirmation of 'Short Read' Noise

'Transcriptome Assembly is Hard', but Not Any More with Richard Smith's Transrate

Efficient Algorithms for de novo Assembly of Alternative Splicing Events from RNA-seq Data

RNAseq - RSEM Group Fights Back

Single-cell RNA-seq Reveals Dynamic Paracrine Control of Cellular Variation

A Novel Machine Learning Method for Orthology Assignment of Whole de novo Assembled Transcriptomes

RNAseq: Estimating Transcript Expression using Min-cost Flow Method

Goodbye RSEM, Sailfish Paper Published

Transcriptome in Vivo Analysis (TIVA) of Spatially Defined Single Cells in Live Tissue

Flexible Isoform-level Differential Expression Analysis with Ballgown

Going Through the Code of SOAPdenovo-trans

Titus Brown's Transcriptome Talk at UC-Davis

What is the True Computing Cost of RNAseq Analysis? - Titus Brown's Slides

TRAPID: Online Tool for Annotation/Analysis of RNAseq Assembly

Cross-post: Is trimming beneficial for RNA-Seq??

SSP Transcriptome Assembler from Tehran, TIGER, PEGASAS Genome Assemblers

CSHL Keynote Talk - Lior Pachter

Today's News - BEETL v0.8 Release and RNA Comparison Papers

Trinity, Oases, SOAPdenovo-trans - Many Helpful Tips from Richard Smith

AfterParty - a Promising Post Processing Tool for Transcriptome Data

Human Transcriptome is Extremely Complex and Snyderome is the Most Complex of All

A Few Good Posts on Transcriptome Assembly and Analysis

RNAseq Annotation Issues - A Good Post by Stuart Brown

Arxiv Paper: Biological Averaging in RNA-Seq

Flux Simulator for RNA-seq Simulation

DEseq and Sailfish Papers for RNAseq

How Novel Ideas Trickle Down from Computer Science to Biology

How Real Are Those 600,000 Spliced Genes in Your Transcriptome Data?

Assessing De Novo Transcriptome Assembly Metrics for Consistency and Utility

SOAPdenovo-Trans Paper Shows the Complexity of Transcriptome Assembly

What Fraction of Genome is Really Functional? (Our lncRNA story)

In Large-scale Biology, Who Has Ownership of the Data?

Rarefaction Curve - Question for Readers

A comparison of Methods for Differential Expression Analysis of RNA-seq Data

Methods to study Event/Isoform Expression and Alternative Splicing from RNA-Seq

Transcriptomic Research around the Globe

A Question on de Bruijn Graphs of Transcriptomes (RNA-seq)

Do We Need to Reinterpret all Published Gene Expression Studies?

Trinity Run Completed. Is This Typical?

An Experience with New Trinity

Few Simple Trinity Tips

Algorithmic Differences between Oases and Trinity

Oases Transcriptome Assembler

  • transcriptome assembly
  • oases
  • velvet
  • RNAseq

Standard Steps for RNAseq Experiment

Two RNAseq Papers - Worm and Sea urchin

Quarterly Growth of Array Express

In our Trends Section

In our Trends Section - II

Can Trinity be Used for Genome Assembly?

  • Trinity
  • genome assembly

Explosion of Transcriptome Data on Drosophila

March 2012 Update on GEO Trends (Countries)

SRA Trends - March 9, 2012

A Strategy for Running Trinity on Very Large NGS Library or Reducing Number of Genes

K-mer Distribution of a Transcriptome

  • de-bruijn
  • transcriptome assembly
  • K-mer

Output of Oases Transcriptome Assembler

  • de-bruijn
  • transcriptome assembly
  • oases
  • velvet

Explaining Output of Trinity Component - Inchworm

  • de-bruijn
  • transcriptome assembly
  • Trinity
  • inchworm

Trinity and Contrail for Color Space

  • de-bruijn
  • transcriptome assembly
  • Trinity
  • genome assembly
  • color space
  • contrail
  • hadoop

GEO and SRA - Quarterly Growth in Transcriptomic Research

  • GEO
  • SRA

De Novo Transcriptome Assemblers – Oases, Trinity, etc. – IV

  • de-bruijn
  • transcriptome assembly
  • oases
  • Trinity

Where are the global hotbeds of transcriptomic research?

  • GEO

De Novo Transcriptome Assemblers – Oases, Trinity, etc. – III

  • de-bruijn
  • transcriptome assembly
  • oases
  • velvet
  • Trinity

De Novo Transcriptome Assemblers – Oases, Trinity, etc. - II

  • de-bruijn
  • transcriptome assembly
  • oases
  • velvet
  • Trinity

Transcriptomic Research around the Globe

A Bird's Eye View of NCBI GEO Database - II

  • GEO

De Novo Transcriptome Assemblers - Oases, Trinity, etc.

  • de-bruijn
  • transcriptome assembly
  • oases
  • velvet
  • Trinity

A Road Map for our Journey through the Transcriptomic Maze

  • introductory
  • bioinformatics

A Bird's Eye View of NCBI GEO Database

  • GEO


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