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Results for "RNA Seq"

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• • LEGE@lege

  

  Comment on "Tools for Differential expression analysis"

  ...n analysis, including: DESeq2: This R package is widely used for analyzing RNA-Seq data. It uses a negative bino...ential expression analysis of RNA-Seq data. It uses a non-param...al expression analysis of RNA-Seq data. It uses a method based...

  435 days ago

• • BioStar@biostar

  

  Comment on "kallisto: a program for quantifying abundances of transcripts from bulk and single-cell RNA-Seq data"

  kallisto can process either single-end or paired-end reads. The default running mode is paired-end and requir...use the --plaintext mode to output plaintext abundance estimates. Alterna...

  1376 days ago

• • LEGE@lege

  

  Comment on "Next Generation Sequencing (NGS) Tutorials"

  Informatics for RNA-seq: A web resource for analysis on the cloud https://github.com/griffithlab/rnaseq_tutorial?

  1588 days ago

• • Jit@jit.aber

  

  Comment on "Running Trinity on RNA-seq !"

  ...logy of your organism based on your assembled transcripts and the input RNA-Seq data. Such studies might incl...ides direct support for several DE analysis methods, including edgeR, DESeq2, Limma/Voom, and ROTS....

  2138 days ago

• • Jit@jit.aber

  

  Comment on "AfterQC: Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data"

  ...N mRIN - Assessing mRNA integrity directly from RNA-Seq data. MultiQC Multi...umerous tools (FastQC, HTSeq, RSeQC, Tophat, STAR, others....es, read length, and frequent sequences. Produces graphical out...n around the data collected. RNA-SeQC RNA-SeQCis a tool w...

  2152 days ago

• • Jitendra Narayan@admin

  

  Comment on "New RNA Seq tool"

  RNA-Seq: a revolutionary tool for transcriptomics http://www.nature.com/nrg/journal/v10/n1/abs/nrg2484.html

  3603 days ago

• • Poonam Mahapatra@poonam

  

  Comment on "New RNA Seq tool"

  GenePattern offers a set of tools to support a wide variety of RNA-seq analyses, including short-read mappin...nbsp;http://www.broadinstitute.org/cancer/software/genepattern/modules/RNA-seq

  3603 days ago

• • John Parker@parker

  

  Comment on "New RNA Seq tool"

  List of RNA-Seq bioinformatics tools http://en.wikipedia.org/wiki/List_of_RNA-Seq_bioinformatics_tools

  3603 days ago

• • Rahul Nayak@rahul

  

  Comment on "List of popular bioinformatics software/tools"

  TopHat http://tophat.cbcb.umd.edu/manual.shtml is a program that aligns RNA-Seq reads to a genome in order to identify exon-exon splice junctions. It is built on the ultrafast short read mapping program Bowtie.

  3663 days ago

• • Jit@jit.aber

  

  Comment on "R and Bioconductor Tutorial"

  ...arches [1] Biostrings – Reading sequences in R [2] BSGenomes &nd...nomes and BioC annotation data [3] DEGSeq – Identify differentially expressed genes from RNA-Seq data. [4] IRanges &ndash...online and other genome browsers. chipseq & ChIPpeakAnno – Ch...

  3685 days ago