[PDF] Top 20 HiC Pro: an optimized and flexible pipeline for Hi C data processing
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HiC Pro: an optimized and flexible pipeline for Hi C data processing
... sequencing data, Hi-C usu- ally requires several millions to billions of paired-end se- quencing reads, depending on genome size and on the desired ...these data thus requires optimized ... See full document
11
MetaWRAP—a flexible pipeline for genome-resolved metagenomic data analysis
... modular pipeline software for shotgun metagenomic data ...metagenomic data processing starting from raw sequencing reads and ending in metagenomic bins and their ...is flexible enough ... See full document
13
CUT&RUNTools: a flexible pipeline for CUT&RUN processing and footprint analysis
... such data proved inadequate due to the lack of an end-to-end computational pipeline specifically tailored to this ...new pipeline, designated CUT&RUNTools, that stream- lines the ... See full document
12
Real-Time Anomaly Detection from Edge to HPC-Cloud
... Anomaly Detection Engine • involves high performance batch and streaming data processing frameworks • detects anomalies from preprocessed data pipeline... • Performance metrics for singl[r] ... See full document
32
FONZIE: An optimized pipeline for minisatellite marker discovery and primer design from large sequence data sets
... Delaruelle C, Detter JC, Deveau A, DiFazio S, Duplessis S, Fraissinet-Tachet L, Lucic E, Frey-Klett P, Fourrey C, Feussner I, Gay G, Grimwood J, Hoegger PJ, Jain P, Kilaru S, Labbé J, Lin YC, Legué V, Le ... See full document
9
Simulations and Modelling for Biological Invasions
... sequence processing pipelines will not know in advance what the appropriate clustering threshold is, as it depends on the relatedness of taxa in their sample, and incorrect assignment of the threshold can be a ... See full document
171
Extending XNAT towards a Cloud-based Quality Assessment Platform for Retinal Optical Coherence Tomographies
... all data processing relies on sufficient data quality, but few tools inherently validate the quality of the input ...image processing, as for example the FreeSurfer pipeline for ... See full document
17
Optimized implementation of digital signal processing applications with gapless data acquisition
... central pro- cessing units (CPUs) together with their streaming single instruction multiple data extensions (SSE) [14] instruction sets to enable fast and accurate jitter ...input data has arrived ... See full document
13
An Overview of Methods for Reconstructing 3-D Chromosome and Genome Structures from Hi-C Data
... raw Hi-C data ob- tained from 3C experiments may contain numerous sys- tematic biases, such as GC content, length of restriction fragments, and mappability between ...pre-process Hi-C ... See full document
20
The effect of data pre processing on optimized training of artificial neural networks
... Nowadays, in the ANN, the high computational cost connected with the learning process of the MLP is a grave problem. This cost is directly linked with the training dataset size. In this study, we proposed to reduce the ... See full document
8
Error, reproducibility and sensitivity : a pipeline for data processing of Agilent oligonucleotide expression arrays
... of data preprocessing for this platform. Using a set of data generated from this array platform, we dissect the major contributors to experimental variability within the ...extract data from Agilent ... See full document
16
Data Processing Models for Distributed Computing and it’s Ecosystem: A Survey
... a data parallel general purpose batch processing ...stream processing engine that can also do micro-batching, the other is a batch processing engine which micro-batches but cannot perform ... See full document
19
Developing automatic ceramic tiles inspection system using the optimized data mining with image processing techniques
... next data mining based classifier is probabilistic neural examines each features present in the feature extraction process using the probability as the training ... See full document
6
A Novel Approach to Implement a High Speed and Low Memory Separable 2D DWT Architecture
... the pipeline showing all the components required by the three ...the data flow shown in this figure comprises only the LL-sub band data necessary for the operations of the ...band data are ... See full document
7
Flexible Data Analysis Pipeline for High-Confidence Proteogenomics.
... Novel Peptides. We identi fi ed 47 potential novel peptides in the C-HPP testis data based on a fi nal set of 210 PSMs generated by our analysis pipeline. We re-evaluated these peptides against an ... See full document
10
ChiCMaxima: a robust and simple pipeline for detection and visualization of chromatin looping in Capture Hi C
... in Hi-C, employs a very simplistic binomial test coupled with multiple test- ing correction to search for overrepresented interactions, but does not explicitly take into account known features of ... See full document
19
The Pipeline of Processing fMRI data with Python Based on the Ecosystem NeuroDebian
... (f)MRI data only provide limited information and feedback about the brain, so data mining is a necessary and significant step for us to get more quantitative and broad functional ...(f)MRI data, ... See full document
13
Design of Image Recognition Accelerator Based on FPGA
... parallel processing of multiple convolutions due to the characteristics of its own serial timing execution ...parallel processing data, and provides a research platform for the design of CNN ... See full document
8
GrapHi C: graph based visualization of Hi C datasets
... hypotheses about how differences in the wild-type and mutant contact maps are reflected in genome organi- zation. On the contrary, the GrapHi-C visualizations (Fig. 2a–d) clearly highlight the loss of structural ... See full document
8
HiFive: a tool suite for easy and efficient HiC and 5C data analysis
... distribution of observed versus unobserved fend inter- actions. A multiplicative modeling approach is used in the analysis software HiCNorm [16]. HiCNorm uses a Poisson regression model using binned counts instead of ... See full document
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