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44 materials found

Scientific topics: Transcriptomics 


Hands-on for 'Trajectory Analysis using Monocle3 ' tutorial

The questions this addresses are:
- How can I prepare input files for Monocle starting from an AnnData object?
- How can I infer lineage relationships between clusters, without a time series?
- What can trajectory analysis tell us?

\nThe objectives are:
- Identify which operations to...

Scientific topics: Transcriptomics

Keywords: transcriptomics, single-cell, trajectory-analysis, paper-replication

Resource type: hands-on tutorial

Slides for 'Trajectory analysis' tutorial

The questions this addresses are:
- What is trajectory analysis?
- What are the main methods of trajectory inference?
- How are the decisions about the trajectory analysis made?
- What to take into account when choosing the method for your data?

\nThe objectives are:
- Become familiar with...

Scientific topics: Transcriptomics

Keywords: transcriptomics

Resource type: slides

Hands-on for 'Combining datasets after pre-processing' tutorial

The questions this addresses are:
- I have some AnnData files from different samples that I want to combine into a single file. How can I combine these and label them within the object?

\nThe objectives are:
- Combine data matrices from different samples in the same experiment
- Label the...

Scientific topics: Transcriptomics

Keywords: transcriptomics, single-cell, 10x, paper-replication, español

Resource type: hands-on tutorial

Hands-on for 'Inferring Trajectories using Python (Jupyter Notebook) in Galaxy' tutorial

The questions this addresses are:
- How can I infer lineage relationships between single cells based on their RNA, without a time series?

\nThe objectives are:
- Execute multiple plotting methods designed to maintain lineage relationships between cells
- Interpret these plots

Scientific topics: Transcriptomics

Keywords: transcriptomics, single-cell, 10x, paper-replication, interactive-tools

Resource type: hands-on tutorial

Hands-on for 'Trajectory Analysis using Python (Jupyter Notebook) in Galaxy' tutorial

The questions this addresses are:
- How can I infer lineage relationships between single cells based on their RNA, without a time series?

\nThe objectives are:
- Execute multiple plotting methods designed to maintain lineage relationships between cells
- Interpret these plots

Scientific topics: Transcriptomics

Keywords: transcriptomics, single-cell, 10x, paper-replication, interactive-tools

Resource type: hands-on tutorial

Hands-on for 'RNA-RNA interactome data analysis' tutorial

The questions this addresses are:
- What are the difficulties in mapping chimeric reads from RNA interactome data?
- How multi mapping is a big problem in these datasets?
- How to filter for meaningful results from large analysis output files?

\nThe objectives are:
- Quality control and...

Scientific topics: Transcriptomics

Keywords: transcriptomics

Resource type: hands-on tutorial

Hands-on for 'Network analysis with Heinz' tutorial

The questions this addresses are:
- Which pathways are potentially contributing to dental caries?

\nThe objectives are:
- Network Analysis of metatranscriptomics data using Heinz in Galaxy to pinpoint the optimal scoring subnetwork.

Scientific topics: Transcriptomics

Keywords: transcriptomics, metatranscriptomics, network analysis

Resource type: hands-on tutorial

Hands-on for 'RNA-Seq analysis with AskOmics Interactive Tool' tutorial

The questions this addresses are:
- How to integrate RNA-Seq results with other datasets using AskOmics?
- How to query these datasets to answer a biological question?
- How to exploit a distant SPARQL endpoint to retrieve information?

\nThe objectives are:
- Launch an AskOmics Interactive...

Scientific topics: Transcriptomics

Keywords: transcriptomics

Resource type: hands-on tutorial

Hands-on for 'Whole transcriptome analysis of Arabidopsis thaliana' tutorial

The questions this addresses are:
- Which miRNAs are upregulated in response to brassinosteroids?
- Which genes are potential target of brassinosteroid-induced miRNAs?

\nThe objectives are:
- Perform miRNA differential expression analysis
- Understand the quasi-mapping-based Salmon method...

Scientific topics: Transcriptomics

Keywords: transcriptomics, miRNA, plants

Resource type: hands-on tutorial

Hands-on for 'De novo transcriptome reconstruction with RNA-Seq' tutorial

The questions this addresses are:
- What genes are differentially expressed between G1E cells and megakaryocytes?
- How can we generate a transcriptome de novo from RNA sequencing data?

\nThe objectives are:
- Analysis of RNA sequencing data using a reference genome
- Reconstruction of...

Scientific topics: Transcriptomics

Keywords: transcriptomics

Resource type: hands-on tutorial

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

The questions this addresses are:
- How to generate a volcano plot from RNA-seq data?

\nThe objectives are:
- Create a volcano plot of RNA-seq data to visualize significant genes

Scientific topics: Transcriptomics

Keywords: transcriptomics

Resource type: hands-on tutorial

Hands-on for 'De novo transcriptome assembly, annotation, and differential expression analysis' tutorial

The questions this addresses are:
- Which biological questions are addressed by the tutorial?
- Which bioinformatics techniques are important to know for this type of data?

\nThe objectives are:
- The learning objectives are the goals of the tutorial
- They will be informed by your audience...

Scientific topics: Transcriptomics

Keywords: transcriptomics

Resource type: hands-on tutorial

Hands-on for 'Visualization of RNA-Seq results with Volcano Plot in R' tutorial

The questions this addresses are:
- How to customise Volcano plot output in R?

\nThe objectives are:
- Learn how to use R to edit Volcano plot colours, points, labels and categories

Scientific topics: Transcriptomics

Keywords: transcriptomics, interactive-tools

Resource type: hands-on tutorial

Hands-on for 'Pre-processing of 10X Single-Cell RNA Datasets' tutorial

The questions this addresses are:
- What is 10X?
- What is STARsolo and what is Cell Ranger?
- What are BCL and MTX files?
- What is an HDF5 file, and why is it important?

\nThe objectives are:
- Demultiplex single-cell FASTQ data from 10X Genomics
- Learn about transparent matrix...

Scientific topics: Transcriptomics

Keywords: transcriptomics, single-cell, 10x

Resource type: hands-on tutorial

Hands-on for '3: RNA-seq genes to pathways' tutorial

The questions this addresses are:
- What are the differentially expressed pathways in the mammary gland of pregnant versus lactating mice?

\nThe objectives are:
- Identification of differentially expressed pathways

Scientific topics: Transcriptomics

Keywords: transcriptomics, mouse

Resource type: hands-on tutorial

Hands-on for 'Pre-processing of Single-Cell RNA Data' tutorial

The questions this addresses are:
- What is single-cell?
- How do we process a batch?
- How do we process multiple batches?
- How do we check for cross-contamination?

\nThe objectives are:
- Demultiplex FASTQ data via UMI-tools
- Understand and validate the extraction of barcodes
-...

Scientific topics: Transcriptomics

Keywords: transcriptomics, single-cell

Resource type: hands-on tutorial

Hands-on for 'CLIP-Seq data analysis from pre-processing to motif detection' tutorial

The questions this addresses are:
- How is raw CLIP-Seq data processed and analysed?
- How do I find binding motifs and targets for a protein (e.g., RBFOX2)?

\nThe objectives are:
- Remove Adapters, Barcodes and Unique Molecular Identifiers (UMIs) from the reads
- Align trimmed reads with...

Scientific topics: Transcriptomics

Keywords: transcriptomics

Resource type: hands-on tutorial

Hands-on for 'Differential abundance testing of small RNAs' tutorial

The questions this addresses are:
- What small RNAs are expressed?
- What RNA features have significantly different numbers of small RNAs targeting them between two conditions?

\nThe objectives are:
- Process small RNA-seq datasets to determine quality and reproducibility.
- Filter out...

Scientific topics: Transcriptomics

Keywords: transcriptomics

Resource type: hands-on tutorial

Hands-on for 'Clustering 3K PBMCs with Scanpy' tutorial

The questions this addresses are:
- What are the steps to prepare single-cell RNA-Seq data for clustering?
- How to cluster cells in single-cell RNA-Seq data?
- How cell type annotation can be assigned to cell clusters?

\nThe objectives are:
- Describe an AnnData object to store single-cell...

Scientific topics: Transcriptomics

Keywords: transcriptomics, single-cell, 10x

Resource type: hands-on tutorial

Hands-on for 'Analysis of plant scRNA-Seq Data with Scanpy' tutorial

The questions this addresses are:
- Can we reclaim cell markers using a different analysis method?
- Are highly variable genes paramount to the analysis?

\nThe objectives are:
- Perform filtering, dimensionality reduction, and clustering
- Generate a DotPlot emulating the original paper...

Scientific topics: Transcriptomics

Keywords: transcriptomics, single-cell, plants, paper-replication

Resource type: hands-on tutorial

Hands-on for 'GO Enrichment Analysis' tutorial

The questions this addresses are:
- How can I functionally interpret a list of genes of interest that I obtained from my experiment?

\nThe objectives are:
- How to perform a GO Enrichment Analysis
- How to interpret and simplify the results

Scientific topics: Transcriptomics

Keywords: transcriptomics

Resource type: hands-on tutorial

Hands-on for '2: RNA-seq counts to genes' tutorial

The questions this addresses are:
- What are the differentially expressed genes in the mammary gland of pregnant versus lactating mice?
- How to analyze RNA count data using limma-voom?
- How to perform quality control (QC) of RNA-seq count data?

\nThe objectives are:
- Analysis of RNA-seq...

Scientific topics: Transcriptomics

Keywords: transcriptomics, limma-voom, mouse, QC

Resource type: hands-on tutorial

Hands-on for '1: RNA-Seq reads to counts' tutorial

The questions this addresses are:
- How to convert RNA-seq reads into counts?
- How to perform quality control (QC) of RNA-seq reads?
- How to do this analysis efficiently in Galaxy?

\nThe objectives are:
- Learn how RNA-seq reads are converted into counts
- Understand QC steps that can be...

Scientific topics: Transcriptomics

Keywords: transcriptomics, collections, mouse, QC

Resource type: hands-on tutorial

Hands-on for 'Single-cell quality control with scater' tutorial

The questions this addresses are:
- How to ensure the quality of single-cell RNA-seq data?
- What are the confounding factors that may affect the interpretation of downstream analyses?

\nThe objectives are:
- Examine scRNA-seq data for low-quality cells
- Visualise data with various types...

Scientific topics: Transcriptomics

Keywords: transcriptomics, single-cell

Resource type: hands-on tutorial

Hands-on for 'Visualization of RNA-Seq results with heatmap2' tutorial

The questions this addresses are:
- How to generate heatmaps from RNA-seq data?

\nThe objectives are:
- Create heatmaps of RNA-seq data

Scientific topics: Transcriptomics

Keywords: transcriptomics

Resource type: hands-on tutorial

Hands-on for 'Downstream Single-cell RNA analysis with RaceID' tutorial

The questions this addresses are:
- What is normalisation and why is it necessary?
- How many types of unwanted variation are there?
- How are biological phenotypes clustered?
- What is the difference between PCA and tSNE?
- What is the difference between cell trajectory and cell...

Scientific topics: Transcriptomics

Keywords: transcriptomics, single-cell

Resource type: hands-on tutorial

Hands-on for 'Small Non-coding RNA Clustering using BlockClust' tutorial

The questions this addresses are:
- What do the read profiles of small non-coding RNAs represent?
- How to cluster the read profiles based on some intrinsic features?

\nThe objectives are:
- Difference between mRNA-seq and smallRNA-seq
- Unsupervised grouping of the adjacent reads into read...

Scientific topics: Transcriptomics

Keywords: transcriptomics

Resource type: hands-on tutorial

Hands-on for 'Reference-based RNAseq data analysis (long)' tutorial

The questions this addresses are:
- How to perform analysis of RNAseq data when reference genome is available?

\nThe objectives are:
- Learns basic concepts of RNAseq analysis

Scientific topics: Transcriptomics

Keywords: transcriptomics

Resource type: hands-on tutorial

Hands-on for 'Generating a single cell matrix using Alevin' tutorial

The questions this addresses are:
- I have some single cell FASTQ files I want to analyse. Where do I start?

\nThe objectives are:
- Generate a cellxgene matrix for droplet-based single cell sequencing data
- Interpret quality control (QC) plots to make informed decisions on cell thresholds
...

Scientific topics: Transcriptomics

Keywords: transcriptomics, single-cell, 10x, paper-replication, español

Resource type: hands-on tutorial

Hands-on for 'Filter, Plot and Explore Single-cell RNA-seq Data' tutorial

The questions this addresses are:
- Is my single cell dataset a quality dataset?
- How do I generate and annotate cell clusters?
- How do I pick thresholds and parameters in my analysis? What's a "reasonable" number, and will the world collapse if I pick the wrong one?

\nThe objectives are:
...

Scientific topics: Transcriptomics

Keywords: transcriptomics, single-cell, 10x, paper-replication, español, interactive-tools

Resource type: hands-on tutorial