![](images/graphics/blank.gif)
Pipeline evaluation
-
Long non-coding RNAs (lncRNAs) are typically expressed at low levels and are inherently highly variable. This is a fundamental challenge for differential expression (DE) analysis. In this study, the performance of 25 pipelines for testing DE in RNA-seq data is comprehensively evaluated, with a particular focus on lncRNAs and low-abundance mRNAs.
16p
vigalileogalilei
27-02-2022
15
1
Download
-
CRISPR/Cas9 pooled screening permits parallel evaluation of comprehensive guide RNA libraries to systematically perturb protein coding sequences in situ and correlate with functional readouts. For the analysis and visualization of the resulting datasets, we develop CRISPRO, a computational pipeline that maps functional scores associated with guide RNAs to genomes, transcripts, and protein coordinates and structures.
19p
vigalileogalilei
27-02-2022
16
1
Download
-
Structural variations (SVs) account for about 1% of the differences among human genomes and play a significant role in phenotypic variation and disease susceptibility. The emerging nanopore sequencing technology can generate long sequence reads and can potentially provide accurate SV identification.
13p
vielonmusk
30-01-2022
10
0
Download
-
Obtaining RNA-seq measurements involves a complex data analytical process with a large number of competing algorithms as options. There is much debate about which of these methods provides the best approach. Unfortunately, it is currently difficult to evaluate their performance due in part to a lack of sensitive assessment metrics.
12p
viaristotle
29-01-2022
6
0
Download
-
We have developed an efficient and inexpensive pipeline for streamlining large-scale collection and genome sequencing of bacterial isolates. Evaluation of this method involved a worldwide research collaboration focused on the model organism Salmonella enterica, the 10KSG consortium.
18p
viarchimedes
26-01-2022
14
1
Download
-
Single-cell RNA-sequencing (scRNAseq) and the set of attached analysis methods are evolving fast, with more than 560 software tools available to the community, roughly half of which are dedicated to tasks related to data processing such as clustering, ordering, dimension reduction, or normalization.
28p
viarchimedes
26-01-2022
10
0
Download
-
In this study, we compared the performance of twelve pipelines (three mapping and four variant discovery algorithms) with recommended settings to capture single nucleotide variants. We observed significant discrepancy in variant calls among tested pipelines for different heterogeneity levels in real and simulated samples with overall high specificity and low sensitivity. Additional to the individual evaluation of pipelines, we also constructed and tested the performance of pipeline combinations.
13p
thiencuuchu
27-11-2021
7
1
Download
-
Populus nigra is a major tree species of ecological and economic importance for which several initiatives have been set up to create genomic resources. In order to access the large number of Single Nucleotide Polymorphisms (SNPs) typically needed to carry out a genome scan, the present study aimed at evaluating RNA sequencing as a tool to discover and type SNPs in genes within natural populations of P. nigra.
12p
viseulgi2711
31-08-2021
6
1
Download
-
The draft genome assemblies produced by new sequencing technologies present important challenges for automatic gene prediction pipelines, leading to less accurate gene models. New benchmark methods are needed to evaluate the accuracy of gene prediction methods in the face of incomplete genome assemblies, low genome coverage and quality, complex gene structures, or a lack of suitable sequences for evidence-based annotations.
20p
vijeeni2711
24-07-2021
13
0
Download
-
We describe a suite of tools and methods that form a core set of capabilities for researchers and clinical investigators to evaluate multiple analytical pipelines and quantify sensitivity and variability of the results while conducting large-scale studies in investigative pathology and oncology.
21p
vioklahoma2711
19-11-2020
16
2
Download
-
Technical advances in Next Generation Sequencing (NGS) provide a means to acquire deeper insights into cellular functions. The lack of standardized and automated methodologies poses a challenge for the analysis and interpretation of RNA sequencing data.
11p
vioklahoma2711
19-11-2020
16
1
Download
-
Manual assessment and evaluation of fluorescent micrograph cell experiments is time-consuming and tedious. Automated segmentation pipelines can ensure efficient and reproducible evaluation and analysis with constant high quality for all images of an experiment.
12p
vioklahoma2711
19-11-2020
8
1
Download
-
The evolution of next-generation sequencing (NGS) technologies has led to increased focus on RNA-Seq. Many bioinformatic tools have been developed for RNA-Seq analysis, each with unique performance characteristics and configuration parameters.
14p
viflorida2711
30-10-2020
12
1
Download
-
Microbiome studies commonly use 16S rRNA gene amplicon sequencing to characterize microbial communities. Errors introduced at multiple steps in this process can affect the interpretation of the data.
12p
viflorida2711
30-10-2020
15
2
Download
-
The results of the study showed that the inlet pressure of the gas compressor reduces as the ambient temperature increases and the increase in the ambient temperature with respect to time of day led to the gas compressor power increase.
17p
cleopatrahuynh
01-06-2020
16
1
Download
-
This paper presents the evaluation of the proposed 4,180km Trans-Saharan Gas Pipeline (TSGP), which is part 2 of this paper. The main aim of this paper was to evaluate the pipeline outlet pressure since a fixed inlet pressure was given and to authenticate the correlation between the performance parameters of gas compressor and pipeline.
14p
cleopatrahuynh
01-06-2020
9
1
Download
-
This paper presents the evaluation of the life cycle cost (LCC) of the natural gas pipeline investment using ‘’techno-economic and environmental risk assessment’’ (TERA) technique. The significance of this paper is to evaluate the cost implication of all the parts of this research work. The selected engines models for the gas compressor drive were developed based on public domain specification, using an inhouse engine performance simulation software: TURBOMATCH.
22p
cleopatrahuynh
01-06-2020
11
1
Download
-
For most organisms, even if their genome sequence is available, little functional information about individual genes or proteins exists. Several annotation pipelines have been developed for functional analysis based on sequence, ‘omics’, and literature data. However, researchers encounter little guidance on how well they perform.
14p
viminato2711
22-05-2020
12
1
Download
-
This study provides a comparison of software pipelines to identify potential mutations by analyzing whole exome sequencing data from cancer patients, which can lead to early detection and prevention of cancer. This information may be useful to other research related to cancer diagnosis using molecular biology and bioinformatics
9p
vixyliton2711
17-04-2019
19
0
Download
-
Pipeline computation, in which a task is decomposed into several stages that are solved sequentially, is a common computational strategy in natural language processing. The key problem of this model is that it results in error accumulation and suffers from its inability to correct mistakes in previous stages. We develop a framework for decisions made via in pipeline models, which addresses these difficulties, and presents and evaluates it in the context of bottom up dependency parsing for English. We show improvements in the accuracy of the inferred trees relative to existing models. ...
8p
hongvang_1
16-04-2013
46
1
Download
CHỦ ĐỀ BẠN MUỐN TÌM
![](images/graphics/blank.gif)