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1609 materials found

Hands-on for 'RNA Seq Counts to Viz in R' tutorial

The questions this addresses are:
- How can I create neat visualizations of the data?

The objectives are:
- Describe the role of data, aesthetics, geoms, and layers in ggplot functions.
- Customize plot scales, titles, subtitles, themes, fonts, layout, and orientation.

Scientific topics: Transcriptomics

Keywords: transcriptomics, interactive-tools

Resource type: hands-on tutorial

Hands-on for 'Reference-based RNA-Seq data analysis' tutorial

The questions this addresses are:
- What are the steps to process RNA-Seq data?
- How to identify differentially expressed genes across multiple experimental conditions?
- What are the biological functions impacted by the differential expression of genes?

The objectives are:
- Check a...

Scientific topics: Transcriptomics

Keywords: transcriptomics, bulk, rna-seq, collections, drosophila, QC, cyoa

Resource type: hands-on tutorial

Hands-on for 'Visualization of RNA-Seq results with CummeRbund' tutorial

The questions this addresses are:
- How are RNA-Seq results stored?
- Why are visualization techniques needed?
- How to select genes for visualizing meaningful results of differential gene expression analysis?

The objectives are:
- Manage RNA-Seq results
- Extract genes for producing...

Scientific topics: Transcriptomics

Keywords: transcriptomics

Resource type: hands-on tutorial

Hands-on for 'Tree thinking for tuberculosis evolution and epidemiology' tutorial

The questions this addresses are:
- What information can I get from a phylogenetic tree?
- How do I estimate a phylogeny?

The objectives are:
- Understand the basic concepts behind phylogenetic trees, as applied to Mycobacterium tuberculosis
- Be able to read and interrogate a phylogeny...

Keywords: evolution, prokaryotes, phylogenetics, evolution, work-in-progress

Resource type: hands-on tutorial

Hands-on for 'Identifying tuberculosis transmission links: from SNPs to transmission clusters' tutorial

The objectives are:
- Create a SNP alignment
- Calculate pairwise SNP distances between MTB samples
- Identify transmission clusters based on SNP distances
- Study the emergence and spread of drug resistance based on transmission analysis.

Keywords: evolution

Resource type: hands-on tutorial

Hands-on for 'A Docker-based interactive Jupyterlab powered by GPU for artificial intelligence in Galaxy' tutorial

The questions this addresses are:
- How to use Jupyterlab and it several features?
- How to use it for creating input datasets and writing artificial intelligence (AI) algorithms?

The objectives are:
- Learn to use Jupyterlab - an online Python editor designed for developing AI algorithms
...

Scientific topics: Statistics and probability

Keywords: statistics, interactive-tools, machine-learning, deep-learning, jupyter-lab, image-segmentation, protein-3D-structure

Resource type: hands-on tutorial

Hands-on for 'PAPAA PI3K_OG: PanCancer Aberrant Pathway Activity Analysis' tutorial

The questions this addresses are:
- How to predict aberrant pathway activity in The Cancer Genome Atlas (TCGA) using Machine learning approaches?

The objectives are:
- Learn to predict aberrant pathway activity using RNA-Seq data, mutational status and copy number variation data from TCGA.
...

Scientific topics: Statistics and probability

Keywords: statistics, Machine learning, Pan-cancer, cancer biomarkers, oncogenes and tumor suppressor genes

Resource type: hands-on tutorial

Hands-on for 'Regression in Machine Learning' tutorial

The questions this addresses are:
- How to use regression techniques to create predictive models from biological datasets?

The objectives are:
- Learn regression background
- Apply regression based machine learning algorithms
- Learn ageing biomarkers and predict age from DNA methylation...

Scientific topics: Statistics and probability

Keywords: statistics

Resource type: hands-on tutorial

Hands-on for 'Classification in Machine Learning' tutorial

The questions this addresses are:
- What is classification and how we can use classification techniques?

The objectives are:
- Learn classification background
- Learn what a quantitative structure-analysis relationship (QSAR) model is and how it can be constructed in Galaxy
- Learn to...

Scientific topics: Statistics and probability

Keywords: statistics

Resource type: hands-on tutorial

Hands-on for 'Text-mining with the SimText toolset' tutorial

The questions this addresses are:
- How can I automatically collect PubMed data for a set of biomedical entities such as genes?
- How can I analyze similarities among biomedical entities based on PubMed data on large-scale?

The objectives are:
- Learn how to use the SimText toolset
-...

Scientific topics: Statistics and probability

Keywords: statistics, interactive-tools

Resource type: hands-on tutorial

Hands-on for 'Machine learning: classification and regression' tutorial

The questions this addresses are:
- what are classification and regression techniques?
- How they can be used for prediction?
- How visualizations can be used to analyze predictions?

The objectives are:
- Explain the types of supervised machine learning - classification and regression.
-...

Scientific topics: Statistics and probability

Keywords: statistics

Resource type: hands-on tutorial

Hands-on for 'Age prediction using machine learning' tutorial

The questions this addresses are:
- How to use machine learning to create predictive models from biological datasets (RNA-seq and DNA methylation)?

The objectives are:
- Learn ageing biomarkers from RNA-seq and DNA methylation datasets
- Apply regression based machine learning algorithms
-...

Scientific topics: Statistics and probability

Keywords: statistics

Resource type: hands-on tutorial

Hands-on for 'Interval-Wise Testing for omics data' tutorial

The questions this addresses are:
- How to visualize high-resolution omics data in different groups of genomic regions?
- How to evaluate differences in high-resolution omics data between groups of genomic regions?
- How to detect locations and scales at which the significant effects...

Scientific topics: Statistics and probability

Keywords: statistics

Resource type: hands-on tutorial

Hands-on for 'Introduction to Machine Learning using R' tutorial

The questions this addresses are:
- What are the main categories in Machine Learning algorithms?
- How can I perform exploratory data analysis?
- What are the main part of a clustering process?
- How can a create a decision tree?
- How can I assess a linear regression model?

The...

Scientific topics: Statistics and probability

Keywords: statistics, interactive-tools

Resource type: hands-on tutorial

Hands-on for 'Image classification in Galaxy with fruit 360 dataset' tutorial

The questions this addresses are:
- How to solve an image classification problem using convolutional neural network (CNN)?

The objectives are:
- Learn how to create a CNN using Galaxy's deep learning tools
- Solve an image classification problem on fruit 360 dataset using CNN in Galaxy

Scientific topics: Statistics and probability

Keywords: statistics

Resource type: hands-on tutorial

Hands-on for 'Basics of machine learning' tutorial

The questions this addresses are:
- What is machine learning?
- Why is it useful?
- What are its different approaches?

The objectives are:
- Provide the basics of machine learning and its variants.
- Learn how to do classification using the training and test data.
- Learn how to use...

Scientific topics: Statistics and probability

Keywords: statistics

Resource type: hands-on tutorial

Hands-on for 'Biomarker candidate identification' tutorial

The questions this addresses are:
- How to mine public databases to retrieve info?
- How to build a selection strategy by applying successive biochemical/cellular criteria to a list of gene/protein?
- How to select biomarkers candidates using experimental information (transcriptomics &...

Scientific topics: Proteomics

Keywords: proteomics, DDA, human

Resource type: hands-on tutorial

Hands-on for 'Clustering in Machine Learning' tutorial

The questions this addresses are:
- How to use clustering algorithms to categorize data in different clusters

The objectives are:
- Learn clustering background
- Learn hierarchical clustering algorithm
- Learn k-means clustering algorithm
- Learn DBSCAN clustering algorithm
- Apply...

Scientific topics: Statistics and probability

Keywords: statistics

Resource type: hands-on tutorial

Hands-on for 'metaQuantome 3: Taxonomy' tutorial

The questions this addresses are:
- How do I look at differentially expressed taxa?
- Can we get top 5 or 10 taxa present in the sample?
- How can I visualize my results?

The objectives are:
- A taxonomy and quantitational analysis of metaproteomic mass spectrometry data.

Scientific topics: Proteomics

Keywords: proteomics, microbiome

Resource type: hands-on tutorial

Hands-on for 'Annotating a protein list identified by LC-MS/MS experiments' tutorial

The questions this addresses are:
- How to filter out technical contaminants?
- How to check for tissue-specificity?
- How to perform enrichment analysis?
- How to map your protein list to pathways (Reactome)?
- How to compare your proteome with other studies?

The objectives are:
-...

Scientific topics: Proteomics

Keywords: proteomics, DDA, human

Resource type: hands-on tutorial

Hands-on for 'MaxQuant and MSstats for the analysis of TMT data' tutorial

The questions this addresses are:
- How to analyze tandem-mass-tag (TMT) labelled shotgun (DDA) data analysis in MaxQuant and MSstats?
- Which proteins are differentially abundant between KMT9α knock-down and control cells?

The objectives are:
- Learn how to use MaxQuant and MSstats for the...

Scientific topics: Proteomics

Keywords: proteomics, DDA, TMT

Resource type: hands-on tutorial

Hands-on for 'Label-free versus Labelled - How to Choose Your Quantitation Method' tutorial

The questions this addresses are:
- What are benefits and drawbacks of different quantitation methods?
- How to choose which quantitation method bests suits my need?

The objectives are:
- Choose your quantitation method.

Scientific topics: Proteomics

Keywords: proteomics, DDA

Resource type: hands-on tutorial

Hands-on for 'Secretome Prediction' tutorial

The questions this addresses are:
- How to predict cellular protein localization based upon GO-terms?
- How to combine multiple localization predictions?

The objectives are:
- Predict proteins in the cellular secretome by using GO-terms.
- Predict proteins in the cellular secretome by...

Scientific topics: Proteomics

Keywords: proteomics, human

Resource type: hands-on tutorial

Hands-on for 'Proteogenomics 1: Database Creation' tutorial

The questions this addresses are:
- How to create a customized Protein Database from RNAseq data?

The objectives are:
- Generating a customized Protein sequence database with variants, indels, splice junctions and known sequences.

Scientific topics: Proteomics

Keywords: proteomics, proteogenomics

Resource type: hands-on tutorial

Hands-on for 'Peptide Library Data Analysis' tutorial

The questions this addresses are:
- How to utilize quantitative properties of amino acids and peptide sequence to analyse peptide data?

The objectives are:
- Calculate descriptors
- Quantitative analysis of peptide sequence properties

Scientific topics: Proteomics

Keywords: proteomics

Resource type: hands-on tutorial

Hands-on for 'Proteogenomics 2: Database Search' tutorial

The questions this addresses are:
- How to identify variant proteoforms in MS data by searching with the customized Protein database?

The objectives are:
- A proteogenomic data analysis of mass spectrometry data to identify and visualize variant peptides.

Scientific topics: Proteomics

Keywords: proteomics, proteogenomics

Resource type: hands-on tutorial

Hands-on for 'Peptide and Protein Quantification via Stable Isotope Labelling (SIL)' tutorial

The questions this addresses are:
- What are MS1 features?
- How to quantify based on MS1 features?
- How to map MS1 features to MS2 identifications?
- How to evaluate and optimize the results?

The objectives are:
- MS1 feature quantitation and mapping of quantitations to peptide and...

Scientific topics: Proteomics

Keywords: proteomics, DDA, SILAC

Resource type: hands-on tutorial

Hands-on for 'metaQuantome 2: Function' tutorial

The questions this addresses are:
- How do I look at differentially expressed proteins?
- How do I get top 5 or 10 function present in the sample?
- How can I visualize my results?

The objectives are:
- A functional and quantitational analysis of metaproteomic mass spectrometry data.

Scientific topics: Proteomics

Keywords: proteomics, microbiome

Resource type: hands-on tutorial

Hands-on for 'metaQuantome 1: Data creation' tutorial

The questions this addresses are:
- How do I perform functional and taxonomy analysis on metaproteomics data?
- How can I perform quantitation on metaproteomics data?
- How do I create inputs that can be used in metaquantome to examine differentially expressed proteins?

The objectives are:
...

Scientific topics: Proteomics

Keywords: proteomics, microbiome

Resource type: hands-on tutorial

Hands-on for 'Peptide and Protein ID using SearchGUI and PeptideShaker' tutorial

The questions this addresses are:
- How to convert LC-MS/MS raw files?
- How to identify peptides?
- How to identify proteins?
- How to evaluate the results?

The objectives are:
- Protein identification from LC-MS/MS raw files.

Scientific topics: Proteomics

Keywords: proteomics, DDA

Resource type: hands-on tutorial