Oqtans: the RNA-seq workbench in the cloud for complete and reproducible quantitative transcriptome analysis

VT Sreedharan, SJ Schultheiss, G Jean… - …, 2014 - academic.oup.com
We present Oqtans, an open-source workbench for quantitative transcriptome analysis, that
is integrated in Galaxy. Its distinguishing features include customizable computational
workflows and a modular pipeline architecture that facilitates comparative assessment of …

[HTML][HTML] Detection of genomic idiosyncrasies using fuzzy phylogenetic profiles

FE Psomopoulos, PA Mitkas, CA Ouzounis - PLoS One, 2013 - journals.plos.org
Phylogenetic profiles express the presence or absence of genes and their homologs across
a number of reference genomes. They have emerged as an elegant representation
framework for comparative genomics and have been used for the genome-wide inference …

[PDF][PDF] Novel Methods for the Computational Analysis of RNA-Seq Data with Applications to Alternative Splicing

A Kahles - 2014 - d-nb.info
Understanding how genetic information is transformed into a diverse spectrum of complex
organisms is one of the longstanding questions of biology. Over the recent years,
advancements in sequencing technology have enabled the accurate measurement of the …

Unix 文本比对分析高通量 RNA⁃ Seq 测序基因表达.

宋东光, 卢博彬, 陈柳婷 - Chinese Journal of Bioinformatics, 2018 - search.ebscohost.com
从RNA⁃ Seq 高通量测序短序列进行比对及拼接获得较长转录本并确定基因表达量的方法随着
转录组测序的广泛开展仍在不断改进, 本文利用类Unix 系统的文本处理命令组合对山茶花开花
期叶片及花瓣的转录组序列进行比对, 序列拼接及其表达量分析. 首先对测序序列进行每1 …

[PDF][PDF] Towards Collaborative Scientific Workflow Management System

G Mostaeen - 2018 - core.ac.uk
The big data explosion phenomenon has impacted several domains, starting from research
areas to divergent of business models in recent years. As this intensive amount of data
opens up the possibilities of several interesting knowledge discoveries, over the past few …

RNA-Seq UD: A bioinformatics plattform for RNA-Seq analysis

M Ramirez, CA Rojas-Quintero… - 2015 10th Iberian …, 2015 - ieeexplore.ieee.org
In this work is presented a process of design and building of a software that gather the tools
required for a RNA-Seq data bioinformatics research. From the proposed a workflow is
proposed that represents all a process that goes through the main stages of the treatment of …

[PDF][PDF] Massive automatic functional annotation mafa

JN Perez-Castillo, CA Rojas-Quintero, N Enrique - 2014 - iwbbio.ugr.es
Functional annotation represents a means to investigate and classify genes and transcripts
according to their function within a given organism. The annotation process for unknown
sequences involves the use and integration of various tools that deal with the following …

Comparison of spliced alignment software in analyzing RNA-Seq data

A Kuosmanen - 2013 - helda.helsinki.fi
A recently developed protocol for sequencing RNA in a cell in a high-throughput manner,
RNA-seq, generates from hundreds of thousands to a few billion short sequence fragments
from each RNA sample. Aligning these fragments, or'reads', to the reference genome in a …

[PDF][PDF] SIBERG User Manual

P Tong, KR Coombes - 2018 - cran.gedik.edu.tr
SIBERG (Systematic Identification of Bimodally ExpRessed Genes using RNAseq data) is an
R package that effectively identifies bimodally expressed genes from RNAseq data based
on Bimodality Index. SIBER models the RNAseq data in the finite mixture modeling …

[PDF][PDF] RNA‐Seq: Methods and Applications

P Thiru - barc.wi.mit.edu
• Total‐count (eg. RPKM)• Upper Quartile (eg. 75th percentile): Similar to Total‐count but per‐
lane upper‐quartile of counts for genes with reads in at least one lane.• Quantile: For each
lane the distribution of read counts is matched to a reference distribution defined in terms of …