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5 results for “Bioinformatic tools”
Benchmarking bioinformatic tools for amplicon-based sequencing of norovirus
<p>This repository contains associated datasets and accession numbers for a study entitled '<strong>Benchmarking bioinformatic tools for amplicon-based sequencing of norovirus'</strong>. The scripts for this project can be found on the GitHub project<a href="https://github.com/ahfitzpa/Benchmarking-bioinformatics-norovirus-amplicons"> page</a>. </p> <p>Expected composition tsv files are the OTU tables for each simulation performed (001-010). OTU IDs in this case are the expected taxonomy with the associated accession numbers. Samples are numbered 1-40, including the simulation number. Expected sequences fasta files contain the sequences used as input for each simulation, without primers or Illumina adapter sequences.</p> <p>Amplicons were generated using the following primers:</p> <p><strong>GI Primers </strong><br> GISKF: CTG CCC GAA TTY GTA AAT GA 4<br> GISKR: CCA ACC CAR CCA TTR TAC A 5<br> <br> <strong>GII Primers </strong><br> G2SKF: CNT GGG AGG GCG ATC GCAA 8<br> G2SKR: CCR CCN GCA TRH CCR TTR TAC AT</p> <p>In this study, three databases and multiple classifiers were compared. Here we include the taxonomy and fasta files for each database; noronet =NoroNet RIVM, calicinet= HuCat CDC and custom, randomly generated database. Fasta files for the classifiers include the GI/GII primers listed above in a 5-3 orientation. </p> <p>The tags.txt file contains the Illumina adapters used for the simulation component of the study.</p>
PhasAGE Training School 1 -Overview of bioinformatics tools for the life sciences & Classification and evolution of non-globular proteins- LECTUREs
<p>The Training School 1 <strong>“Computational Methods to Study Protein Phase Separation”</strong> is the first edition of a series of PhasAGE training activities.</p> <p>The goal of this course is to provide participants with the basic knowledge to understand the phenomenon of <strong>Phase Separation</strong>, its role in biological processes and diseases. In addition, the course will provide <strong>an overview of the available computational resources</strong> to navigate this knowledge. Participants will have <strong>hands-on training</strong> in tools and resources available for life sciences, to collect information from the literature on biomolecular phase transitions, identify features triggering phase transitions, mutations associated with diseases, known or predicted PTMs and molecular interaction sites.</p>
Supplementary Materials for Discovery of Hub Genes and Construction of Competitive Endogenous RNA Network in Human Cytomegalovirus Infection Using Computational and Bioinformatics Tools
<p><span>Table S1: List of targeted genes by 41 differentially expressed microRNAs (DEMs) agreed in Targetscan and miRDB; Table S2: Significant biological process (BP) of 144 genes associated with Human Cytomegalovirus (HCMV); Table S3: Significant cellular components (CC) of 144 genes associated with HCMV; Table S4: Enriched molecular function (MF) of 144 genes associated with HCMV; Table S5: Pathways significantly affected by 144 genes in HCMV; Figure S1: Number of interactions for each gene in protein-protein interaction (PPI) network.</span></p>
metabarcoding data for: Benchmark of bioinformatics tools for fast and accurate species identification from environmental DNA metabarcoding
Open the record for dataset details and reuse information.
Evaluation of somatic copy number variation detection by NGS techonologies and bioinformatics tools
GEO Series GSE212051. Homo sapiens. 6 samples. Type: Genome variation profiling by SNP array.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.