RNA-‐Seq data processing and quality control
Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R
... biological data ana- lysis through the Bioconductor project ( Huber et ...bulk RNA-seq data, the existing data structures (like the ExpressionSet class) are not sufficient for ...
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An RNA-Seq bioinformatics pipeline for data processing of Arabidopsis thaliana datasets
... Results of PPI network analysis shows most of the DEGs during the transition phase regulate 532. other DEGs which provide induced resistance and protection against ex[r] ...
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DATA PROCESSING AND QUALITY CONTROL
... the data are derived from recording or totalizing gauges, first priorities are the apportionment of accumulated rainfall totals and the interpolation of missing ...interval data from recording gauges; ...
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Bioinformatics for RNA‐Seq Data Analysis
... degraded RNA. After quality and quantity of the RNA samples have been addressed, one must then choose whether to profile the total RNA space or the mRNA space ...most RNA‐seq ...
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RNA-seq data analysis pipeline
... typical RNA-seq data analyis ...general RNA-seq data analysis pipeline using specific tools; completed an example pipeline by using data from a public database and ...
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SCRABBLE: single cell RNA seq imputation constrained by bulk RNA seq data
... bulk RNA-seq data to im- pute dropout data in order to reduce unwanted bias during ...experimental data suggests that SCRABBLE achieves significant improvement in terms of recovering ...
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Classification of low quality cells from single cell RNA seq data
... package. Data availability To ease usability, we developed an R package, which contains functions to extract all necessary classification fea- tures from single-cell gene expression ...low quality cells by ...
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NGS Data Analysis: An Intro to RNA-Seq
... some quality control checks on raw sequence data coming from high throughput sequencing ...your data has any problems of which you should be aware before doing any further ...
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Re-using public RNA-Seq data
... the data and processing ...manages data, recollects results and tracks ...its processing task which existing solutions effectively fail to ...
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GC-Content Normalization for RNA-Seq Data
... benchmarking RNA-Seq datasets for two types of human reference samples from the MicroArray Quality Control (MAQC) Project ...exploratory data analysis and normalization methods proposed ...
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Computational analysis of bacterial RNA-Seq data
... gonorrhoeae RNA-seq experiments. The N. gonorrhoeae RNA-seq experiments, in contrast to our RNA-seq experiments in other bacteria, generated a shorter read length (36 nt as ...
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Modular and efficient pre-processing of single-cell RNA-seq
... for each dataset, using the estimated per-base error rate . UMI collision estimates A UMI associated with a read from a cell is said to have “collided” if it appears in two or more reads originating from different ...
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CHANCE: comprehensive software for quality control and validation of ChIP seq data
... the quality control step of ChIP- seq ...the quality of a ChIP-seq data set, it allows experimentalists to compute multiple quality metrics, and it generates informative ...
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Quality assessment and control of tissue specific RNA-seq libraries of Drosophila transgenic RNAi models
... during quality control analysis, can increase the coverage of pro- tein coding genes, causing a change in the number of DE genes, mostly likely to a decrease of incurred sampling ...
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Computational Methods for CLIP-seq Data Processing
... AbstrAct: RNA-binding proteins (RBPs) are at the core of post-transcriptional regulation and thus of gene expression control at the RNA ...the RNA regions recognized by RBPs on a ...
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Challenges Analyzing RNA Seq Gene Expression Data
... quencing) data is very ...Transform RNA- sequencing count data to a continuous variable or continue to work with count ...each data type, analysis tools have been developed and seem ...
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A Novel Assembly Algorithm That Optimizes For RNA-Seq Data
... Figure 15. Structure glink and klink. Based on “short read ->k-mers” array, the program can find all k-mers from a short read. For each k-mer, the program checks the “k-mer->short reads” array to find all other short ...
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A survey of best practices for RNA seq data analysis
... Gene fusion discovery The discovery of fused genes that can arise from chromosomal rearrangements is analogous to novel iso- form discovery, with the added challenge of a much lar- ger search space as we can no longer ...
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FastqPuri: high-performance preprocessing of RNA-seq data
... Discussion RNA-seq is currently widely used to assess transcript and gene expression lev- ...sequence data quality control and preprocessing the most time demanding steps in data ...
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Zero-Inflated Models for RNA-Seq Count Data
... our data where we fit PMM, ZIPMM, NBMM, and ZINBMM ...To control FDR, we compute Benjamini-Hochberg (BH) (Benjamini and Hochberg, 1995) adjusted ...in RNA-seq data analysis while ...
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