We propose a bioinformatics pipeline framework for DNA sequencing analysis. This pipeline is a solution for the rapid and efficient deployment of the workflow pipeline to institutions and laboratories, allowing reproducible results based on virtual machine technologies. It is capable of supporting the ...
Isomap62,63,64, can also be utilized.t-SNE is implemented in the popular Cell Ranger pipeline (10× Genomics) and in Seurat (http://satijalab.org/seurat/) in the R package. Although LLE and Isomap demonstrate superior performance for microarray data65, these methods should be further evalua...
A Bioinformatics Pipeline for Whole Exome Sequencing: Overview of the Processing and Steps from Raw Data to Downstream Analysis. bioRxiv, 2017: 201145. Oakeson K F, Wagner J M, Mendenhall M, et al. Bioinformatic analyses of whole-genome sequence data in a public health laboratory. Emerging ...
Isomap62,63,64, can also be utilized.t-SNE is implemented in the popular Cell Ranger pipeline (10× Genomics) and in Seurat (http://satijalab.org/seurat/) in the R package. Although LLE and Isomap demonstrate superior performance for microarray data65, these methods should be further evalua...
The x-axis contains pipeline numbers from Table 1 Full size image We next defined properties of the discordant SNVs. The discordant SNVs that were not detected from alignment directly to the target version are hence named “position discordant SNVs”. The discordant SNVs that were identified ...
docker groovy hello aws cloud bioinformatics pipeline nextflow hpc reproducible-research workflow-engine slurm pipeline-framework sge singularity reproducible-science dataflow singularity-containers Updated May 27, 2025 Groovy sokrypton / ColabFold Star 2.2k Code Issues Pull requests Making Protein foldi...
The ECCsplorer pipeline (Fig. 1a; Additional file 1: Fig. S1) is modular and implemented in Python 3 and partly in R [19]. The ECCsplorer pipeline provides a framework for the automated detection of eccDNA candidates using well established tools including data transfer between tools, data sum...
It is a conversion of viralevo DSL1 pipeline to DSL2. DSL1 viralevo pipeline was originally written by: @bleazard, @lescai, @MartinFritzsche and @PedroRaposo. Citations You can cite the nf-core publication as follows: The nf-core framework for community-curated bioinformatics pipelines. ...
Worked with Daniel Weinberger and Kristen K. Nicodemus. Wrote an automated statistical analysis pipeline for candidate gene studies. Wrote software to visualize the results of SNP analyses. Performed analysis in a simulation study assessing power and type I error of single SNP transmission disequilibrium...
interactions in the microbial communities examined. To facilitate its application by the scientific community, all these methods and statistical tools have been integrated into a comprehensive Molecular Ecological Network Analysis Pipeline (MENAP), which is open-accessible now (http://ieg2.ou.edu/MENA...