[PDF] Top 20 Automated, highly scalable RNA-seq analysis
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Automated, highly scalable RNA-seq analysis
... RNA-sequencing (RNA-seq) has largely supplanted array-based methods for infer- ring differential expression at the gene, isoform and event level as RNA-seq is more s[r] ... Voir le document complet
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Wide cross-species RNA-Seq comparison reveals a highly conserved role for Ferroportins in nickel hyperaccumulation in plants
... of RNA-Seq technologies has opened the possibility to study non-model species at the molecular ...transcriptomics analysis and COG annotation to identify genes associated with nickel ... Voir le document complet
22
SimBA: A methodology and tools for evaluating the performance of RNA-Seq bioinformatic pipelines
... assessed RNA-Seq alignment tools on three human and malaria datasets at the read, junction and base ...that highly-expressed junc- tions have more weight in the junction-level analysis than ... Voir le document complet
15
Systematic analysis of TruSeq, SMARTer and SMARTer Ultra-Low RNA-seq kits for standard, low and ultra-low quantity samples.
... low RNA inputs 17 , 19 – 21 and some studies have focused on both aspects 17 , 18 , or on the general properties of the RNA-seq protocols 3 ...in RNA-seq library protocols, we use human ... Voir le document complet
13
CLIFinder: Identification of LINE-1 Chimeric Transcripts in RNA-seq data
... for highly represented chimeras and that the analysis of different samples together allows assessing precisely LCT expression genome-wide in a specific ... Voir le document complet
9
Deep RNA-Seq reveals miRNome differences in mammary tissue of lactating Holstein and Montbéliarde cows
... our analysis allowed us to detect only 16 predicted miRNAs, whereas the use of a BLAST strategy identified 2823 and 2286 po- tential miRNAs in Jinhua and Yorkshire breeds, re- ...was highly expressed in MG ... Voir le document complet
12
dearseq: a variance component score test for RNA-Seq differential analysis that effectively controls the false discovery rate
... for RNA-seq data, b) a highly non-linear model designed to violate most modeling assumptions, and c) a re- sampling from SEQC data [18] with truncated Gaussian ...for RNA-seq count ... Voir le document complet
22
SNP calling from RNA-seq data without a reference genome: identification, quantification, differential analysis and impact on the protein sequence
... Sequencing errors may generate bubbles in the DBG. A distinctive feature that helps to discriminate them from true variants is that one path of the bubble is expected to be poorly covered. In practice, a common way to ... Voir le document complet
14
An efficient RNA-seq-based segregation analysis identifies the sex chromosomes of Cannabis sativa
... we RNA-sequenced a ...segregation analysis for all ...Further analysis of the sex-linked genes revealed that ...large, highly divergent nonrecombining regions, yet still be roughly ... Voir le document complet
11
Comprehensive Identification and Spatial Mapping of Habenular Neuronal Types Using Single-Cell RNA-Seq
... (detailed analysis in Figure 4) ...select highly variable genes, we used two approaches: (1) A variable gene selection method implemented in Seurat [31], and (2) an alternative approach that ranks genes ... Voir le document complet
40
CEL-Seq2: sensitive highly-multiplexed single-cell RNA-Seq
... Expression analysis pipeline CEL-Seq reads were processed into an expression matrix using a multistep, parallel computational pipeline within the Galaxy framework ...the analysis time by roughly the ... Voir le document complet
8
RNA-Seq Analysis of an Antisense Sequence Optimized for Exon Skipping in Duchenne Patients Reveals No Off-Target Effect
... the analysis of potential off-target effects induced by an antisense sequence designed for exon ...and analysis time, we propose a relevant transgene-specific in vitro toxicology study for exon-skip- ... Voir le document complet
16
RNA-Seq Analysis of an Antisense Sequence Optimized for Exon Skipping in Duchenne Patients Reveals No Off-Target Effect.
... through RNA-Seq and In Silico Target Predictions We previously showed through biodistribution analysis of the vector in GRMD dogs that skeletal muscle and liver were the most trans- duced tissues ... Voir le document complet
15
Comparison of normalization methods for differential gene expression analysis in RNA-Seq experiments: A matter of relative size of studied transcriptomes
... First, methods directly addressing this issue are taken into consideration. The Trimmed Mean of M-values (TMM) method (developed in ref. 11) deals with estimating the “relative RNA production of 2 samples” under ... Voir le document complet
10
Highly scalable parallel simulator of a host-parasite system
... L’archive ouverte pluridisciplinaire HAL, est destinée au dépôt et à la diffusion de documents scientifiques de niveau recherche, publiés ou non, émanant des établissements d’enseignemen[r] ... Voir le document complet
39
RNA-seq analysis of hepatic gene expression of common Pekin, Muscovy, mule and hinny ducks fed ad libitum or overfed
... the RNA Seq study. OB and DE generated RNA libraries, sequencing and quality controls of RNA sequences ...for RNA Seq preprocessing, sequence assembly and gene expression ...out ... Voir le document complet
15
Decoupling genetics, lineages, and microenvironment in IDH-mutant gliomas by single-cell RNA-seq
... dehydration. RNA targets in dewaxed sections were unmasked by treating with pretreatment buffer at 95°C for 10 min and digested with 1:100 dilution protease at 40°C for 10 min, followed by fixation with 10% ... Voir le document complet
30
Automated analysis of Stateflow models
... 5.1 CoCoSim CoCoSim [ 17 ] is an open source automated logic-based analysis framework for Simulink models. CoCoSim consists of two main components: (i) a compiler that compiles a subset of Simulink models ... Voir le document complet
19
RADIS: analysis of RAD-seq data for interspecific phylogeny
... Cruaud et al., 2014 ; Eaton and Ree, 2013 ; Hipp et al., 2014 ; McCluskey and Postlethwait, 2015 ). However, analyzing RAD-seq data to infer phylogenies remains challenging as it requires many steps and decisions ... Voir le document complet
3
Automated analysis of musical structure
... This dissertation was originally motivated by the author's Master's thesis work of building a query-by-humming system, which allows the users to search for music b[r] ... Voir le document complet
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