Article Archive

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Formula Syntax in RNAseq Packages like DESeq2 or edgeR

Rnaseq.work - Current APIs and Design Decisions

Rnaseq.work - Plotting Functions in RNAseq-related Packages

Rnaseq.work - A Package with Clean APIs for Statistical Analysis of RNAseq Data

Live Online Class - RNAseq Data Analysis using R

GRASS for Rapid Reannotation of RNAseq Data

SuperTranscript - a reference for analysis and visualization of the transcriptome

Lior Pachter's Zika Paper

Trimming of sequence reads alters RNA-Seq gene expression estimates

Boiler: Lossy compression of RNA-seq alignments using coverage vectors

They lost half of the DATA !

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

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

Accurate, fast, and model-aware transcript expression quantification with Salmon

RapMap - Rob Patro's Reimplements Kallisto's Pseudoalignment Code

Will I Use Kallisto? Definitely, Most Likely and Never

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

NASA Predicts Dope Will be Legalized in Entire USA by 2025 :)

How Much Should a Poor Scientist Pay to Access Old Research Papers?

Getting the Most Out of RNA-seq Data Analysis

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

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

Lightweight Algorithms for RNAseq Expression Analysis - Sailfish, Kallisto

Pachter Blogs on Sailfish vs Kallisto

Evaluation of tools for differential gene expression analysis by RNA-seq on

Kallisto from Pachterlab for RNAseq Quantification

Why Weight? Modelling Sample and Observational Level Variability Improves Power

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

Utilizing de Bruijn graph of metagenome assembly for metatranscriptome analysis

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

RNA-guided gene drives can efficiently and reversibly bias inheritance in wild

rnaQUAST: Quality Assessment Tool for Transcriptome Assemblies

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

Highly-efficient Cas9-mediated transcriptional programming

Comparisons of computational methods for differential alternative splicing

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

MUSiCC for Metagenomes and Lior Pachter's Code for Transcriptomes

High-Resolution Transcriptome Analysis with Long-Read RNA Sequencing

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

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

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

Efficient Algorithms for de novo Assembly of Alternative Splicing Events from

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

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

Flexible Isoform-level Differential Expression Analysis with Ballgown

Titus Brown's Transcriptome Talk at UC-Davis

Good C++ Development Practices in Sailfish Code

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

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

Cause of Heart Disease in Salmon Solved with Next-gen Sequencing, but....

Flux Simulator for RNA-seq Simulation

DEseq and Sailfish Papers for RNAseq

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

Assessing De Novo Transcriptome Assembly Metrics for Consistency and Utility

RNA-seq Data on Prostate Cancer Publicly Available from BGI

SOAPdenovo-Trans Paper Shows the Complexity of Transcriptome Assembly

CoRAL: Predicting Non-coding RNAs from Small RNA-sequencing Data

TopHat2: Accurate Alignment of Transcriptomes in the Presence of Insertions, Deletions and Gene Fusions

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

Methods to study Event/Isoform Expression and Alternative Splicing from

Isolation and Characterization of RNA-Containing Exosomes

Prediction of novel long non-coding RNAs based on RNA-Seq data of mouse Klf1

Transcriptomic Research around the Globe

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

STAR: Really Kick-ass RNA-seq Aligner

Many RNA-seq Presentations/Posters at ASHG Conference, San Francisco

Trinity Run Completed. Is This Typical?

An Experience with New Trinity

Few Simple Trinity Tips

Algorithmic Differences between Oases and Trinity

Oases Transcriptome Assembler

Analysis of NGS miRNA Data – a Paired-ended Library

Standard Steps for RNAseq Experiment

Sequencing miRNAs with NGS Technology

Analysis of NGS miRNA Library - an Example

Two RNAseq Papers - Worm and Sea urchin

Quarterly Growth of Array Express

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

Custom Array Experiment - Complete Pipeline

K-mer Distribution of a Transcriptome

Output of Oases Transcriptome Assembler

Explaining Output of Trinity Component - Inchworm

Trinity and Contrail for Color Space

Using Hadoop for Transcriptomics - An Example to Get Started

GEO and SRA - Quarterly Growth in Transcriptomic Research

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

Where are the global hotbeds of transcriptomic research?

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

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

Transcriptomic Research around the Globe

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

De Novo Transcriptome Assemblers - Oases, Trinity, etc.

De Bruijn Graphs for Alternative Splicing and Repetitive Regions

Using Hadoop for Transcriptomics

A Road Map for our Journey through the Transcriptomic Maze

Using R for Transcriptome Analysis - I

A Bird's Eye View of NCBI GEO Database

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