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Data analysis workflows
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The DNA metabarcoding approach has become one of the most used techniques to study the taxa composition of various sample types. To deal with the high amount of data generated by the high-throughput sequencing process, a bioinformatics workflow is required and the QIIME2 platform has emerged as one of the most reliable and commonly used.
14p
vihagrid
30-01-2023
8
3
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Velocity model technique is routinely used to convert data from the time-to-depth domain to support prospect evaluation, reservoir modelling, well engineering, and further drilling operation. In Vietnam, the conventional velocity model building workflow oversimplifies the interval velocities as only well interval velocities are populated into 2D grids for depth conversion or oversimplified calibration interval velocities by applying a single scaling factor function.
7p
viharry
14-12-2022
8
4
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Sequencing errors are key confounding factors for detecting low-frequency genetic variants that are important for cancer molecular diagnosis, treatment, and surveillance using deep next-generation sequencing (NGS). However, there is a lack of comprehensive understanding of errors introduced at various steps of a conventional NGS workflow, such as sample handling, library preparation, PCR enrichment, and sequencing. In this study, we use current NGS technology to systematically investigate these questions.
15p
vigalileogalilei
27-02-2022
14
2
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Vector-borne diseases (VBDs) impact both human and veterinary medicine and pose special public health challenges. The main bacterial vector-borne pathogens (VBPs) of importance in veterinary medicine include Anaplasma spp., Bartonella spp., Ehrlichia spp., and Spotted Fever Group Rickettsia.
10p
vidarwin
23-02-2022
11
1
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We present the software Condition-specific Regulatory Units Prediction (CRUP) to infer from epigenetic marks a list of regulatory units consisting of dynamically changing enhancers with their target genes. The workflow consists of a novel pre-trained enhancer predictor that can be reliably applied across cell types and species, solely based on histone modification ChIP-seq data.
23p
vielonmusk
30-01-2022
12
0
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Existing workflows for the analysis of multi-omic microbiome datasets are lab-specific and often result in sub-optimal data usage. Here we present IMP, a reproducible and modular pipeline for the integrated and reference-independent analysis of coupled metagenomic and metatranscriptomic data.
21p
vialfrednobel
29-01-2022
9
0
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High-throughput CRISPR screens have shown great promise in functional genomics. We present MAGeCK-VISPR, a comprehensive quality control (QC), analysis, and visualization workflow for CRISPR screens. MAGeCK-VISPR defines a set of QC measures to assess the quality of an experiment, and includes a maximum-likelihood algorithm to call essential genes simultaneously under multiple conditions.
13p
viaristotle
29-01-2022
12
0
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Lecture UML based modeling and analysis: Detailing use cases scenarios and workflows present the content: main success scenario, other scenarios (successes or failures), user management, register user, organization of use case models, UML 2.0 activity diagrams, process order, data flow and control flow, dataflow networks, partitioning of activities,...
21p
bachkhinhdaluu
03-12-2021
18
0
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The workflow or framework includes the following steps: data processing, sequence clustering, taxonomic assignment, and data visualization. Moreover, we also like to catch readers’ attention to the information about bacterial communities living in the ocean as most marine microorganisms are unculturable, especially residing in coral reefs, namely, bacteria are associated with the coral Acropora tenuis in this case.
11p
spiritedaway36
25-11-2021
8
1
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Exploration of large data sets, such as shotgun metagenomic sequence or expression data, by biomedical experts and medical professionals remains as a major bottleneck in the scientific discovery process. Although tools for this purpose exist for 16S ribosomal RNA sequencing analysis, there is a growing but still insufficient number of user-friendly interactive visualization workflows for easy data exploration and figure generation. The development of such platforms for this purpose is necessary to accelerate and streamline microbiome laboratory research.
11p
vibeauty
23-10-2021
10
1
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Next-Generation Sequencing (NGS) has been widely accepted as an essential tool in molecular biology. Reduced costs and automated analysis pipelines make the use of NGS data feasible even for small labs, yet the methods for interpreting the data are not sophisticated enough to account for the amount of information.
12p
vigiselle2711
30-08-2021
11
1
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Recent advancements in in situ gene expression technologies constitute a new and rapidly evolving field of transcriptomics. With the recent launch of the 10x Genomics Visium platform, such methods have started to become widely adopted. The experimental protocol is conducted on individual tissue sections collected from a larger tissue sample.
7p
vijeeni2711
24-07-2021
9
0
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High-throughput transcriptomic datasets are often examined to discover new actors and regulators of a biological response. To this end, graphical interfaces have been developed and allow a broad range of users to conduct standard analyses from RNA-seq data, even with little programming experience.
15p
vilichoo2711
23-06-2021
10
1
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Cheminformaticians have to routinely process and analyse libraries of small molecules. Among other things, that includes the standardization of molecules, calculation of various descriptors, visualisation of molecular structures, and downstream analysis.
4p
viwyoming2711
16-12-2020
8
1
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Next-generation sequencing (NGS) technologies have resulted in petabytes of scattered data, decentralized in archives, databases and sometimes in isolated hard-disks which are inaccessible for browsing and analysis. It is expected that curated secondary databases will help organize some of this Big Data thereby allowing users better navigate, search and compute on it.
18p
vikentucky2711
26-11-2020
10
0
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Mandatory deposit of raw microarray data files for public access, prior to study publication, provides significant opportunities to conduct new bioinformatics analyses within and across multiple datasets.
11p
vikentucky2711
26-11-2020
11
0
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A common class of biomedical analysis is to explore expression data from high throughput experiments for the purpose of uncovering functional relationships that can lead to a hypothesis about mechanisms of a disease. We call this analysis expression driven, −omics hypothesizing.
12p
vikentucky2711
26-11-2020
7
0
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Ongoing advancements in cloud computing provide novel opportunities in scientific computing, especially for distributed workflows. Modern web browsers can now be used as high-performance workstations for querying, processing, and visualizing genomics’ “Big Data” from sources like The Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC) without local software installation or configuration.
12p
vikentucky2711
26-11-2020
11
0
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Although the costs of next generation sequencing technology have decreased over the past years, there is still a lack of simple-to-use applications, for a comprehensive analysis of RNA sequencing data. There is no one-stop shop for transcriptomic genomics.
11p
vikentucky2711
26-11-2020
10
1
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Phylogenetic tools and ‘tree-thinking’ approaches increasingly permeate all biological research. At the same time, phylogenetic data sets are expanding at breakneck pace, facilitated by increasingly economical sequencing technologies.
9p
vikentucky2711
26-11-2020
6
0
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