This online workshop is hosted by Genomics Aotearoa and NeSI. The workshop will be taught from 10:00am-4:00pm NZT on the 16th of April 2024. It is for New Zealand researchers interested in progressing their abilities with Shell. The workshop will cover Shell overview, downloading and verifying data, inspecting and manipulating text data with Unix tools, automating file-processing.

This will include:

• An overview of the Shell, UNIX and Linux.
• Downloading data from a remote source and checking data integrity.
• Recap navigating files and directories, and commands used in routine tasks.
• Inspecting and manipulating data, part 1 (the head, less, grep, and sed commands).
• Inspecting and manipulating data, part 2 (using awk and bioawkto process text).
• Automating file processing.
• Challenges: solve example molecular biology problems using shell scripts.

This workshop assumes some familiarity with Shell. You will need to be able to do the following tasks via command line:

• Navigating files and directories.
• An understanding on full versus relative paths.
• Working with files and directories (examining files, creating, copying, moving and removing).
• Use a command line-based text editor such as nano.

And have a basic understanding of:

• File/directory permission in Linux.
• For loops (preferred, not required).

If you lack the above skills, you can use these sites as a refresher: Introduction to Command Line Carpentries lesson https://datacarpentry.org/shell-genomics/

Setup
This is a fully online, hands-on workshop. The workshop material will be run on the NeSI High Performance Computing (HPC) platforms – there is no need to install any software for this workshop. Instructions on how to access the NeSI HPC service will be sent out with the confirmation letter to registrants.

You can view the workshop material, including the objectives and content here.

Participants must have their own machine to work on and plan to participate actively in the workshop. You will require a working web browser.

Register for this workshop at Eventbrite.

If you have any questions about these workshops, including whether they are suitable for you, please contact tyler.mcinnes@otago.ac.nz.

Webinar

Speaker:

Dr. Myriam El Khawand leads the customer success team at Dovetail Genomics and has been with the company for over 5 years helping customers achieve their research goals using Dovetail proximity ligation kits and analysis solutions.

• Introduction to spectral and traditional flow cytometry and data analysis (Session 1)
• Considerations for Spectral Flow Cytometry Sample Preparation (Session 1/2)
• Designing and optimising a multi-colour panel (Session 2)

Genomics Aotearoa is again holding its annual meeting of postdocs and early career researchers, organised by Training Coordinator Tyler McInnes. This year’s meeting in Wellington on May1-2 spans two days and includes a diverse spread of workshops and networking events.

More details to come.

This workshop, taught by Professor Mik Black, will introduce skills and tools required for the analysis of single-cell RNA-seq data (scRNA-seq data) in R. The workshop will be taught online over four half-days, on May 8^th, 9^th, 15^th and 16^th  (9am – 1pm). You should attend all 4 sessions.

This is an advanced workshop which requires an intermediate level of R knowledge and experience. To participate in this workshop you must have either completed the Genomics Aotearoa Intermediate R workshop, or have an equivalent level of experience (e.g., be a semi-regular R user). Because of the complexity of this workshop we will not have the time or resources to solve coding errors. However, the focus of this workshop will be on the concepts and discussion of the statistical methodology rather than your ability to code quickly.

Because we expect a high level of interest in this workshop and we have limited spaces, we are inviting expressions of interest no later than Friday April 26^th and will select a group of attendees based on needs and experience. We will endeavour to maximise the overall positive impact on research in Aotearoa and distribute this training as fairly as possible. You will be advised whether you are able to attend the training by end of day Monday April 29^th. 

If we are not able to offer you a space in this training, you will be kept informed about future options for scRNA-seq training.

What will this workshop cover?

• Alignment and feature counting with Cell Ranger (briefly).
• QC and exploratory analysis.
• Normalisation.
• Sctransform: Variant Stabilising transformation.
• Feature selection and dimensionality reduction.
• Batch correction and data set integration.
• Clustering.
• Identification of cluster marker genes.
• Differential gene expression analysis.
• Differential abundance.

*Note that some of this material may be mentioned only briefly due to time constraints, in which case you will be pointed towards supplementary material for self-guided learning.

If you have any questions about this workshop, please contact Genomics Aotearoa Training Coordinator Dr Tyler McInnes (tyler.mcinnes@otago.ac.nz).

This workshop, taught by Professor Mik Black, will introduce skills and tools required for the analysis of single-cell RNA-seq data (scRNA-seq data) in R. The workshop will be taught online over four half-days, on May 8^th, 9^th, 15^th and 16^th  (9am – 1pm). You should attend all 4 sessions.

This is an advanced workshop which requires an intermediate level of R knowledge and experience. To participate in this workshop you must have either completed the Genomics Aotearoa Intermediate R workshop, or have an equivalent level of experience (e.g., be a semi-regular R user). Because of the complexity of this workshop we will not have the time or resources to solve coding errors. However, the focus of this workshop will be on the concepts and discussion of the statistical methodology rather than your ability to code quickly.

Because we expect a high level of interest in this workshop and we have limited spaces, we are inviting expressions of interest no later than Friday April 26^th and will select a group of attendees based on needs and experience. We will endeavour to maximise the overall positive impact on research in Aotearoa and distribute this training as fairly as possible. You will be advised whether you are able to attend the training by end of day Monday April 29^th. 

If we are not able to offer you a space in this training, you will be kept informed about future options for scRNA-seq training.

What will this workshop cover?

• Alignment and feature counting with Cell Ranger (briefly).
• QC and exploratory analysis.
• Normalisation.
• Sctransform: Variant Stabilising transformation.
• Feature selection and dimensionality reduction.
• Batch correction and data set integration.
• Clustering.
• Identification of cluster marker genes.
• Differential gene expression analysis.
• Differential abundance.

*Note that some of this material may be mentioned only briefly due to time constraints, in which case you will be pointed towards supplementary material for self-guided learning.

If you have any questions about this workshop, please contact Genomics Aotearoa Training Coordinator Dr Tyler McInnes (tyler.mcinnes@otago.ac.nz).

This workshop, taught by Professor Mik Black, will introduce skills and tools required for the analysis of single-cell RNA-seq data (scRNA-seq data) in R. The workshop will be taught online over four half-days, on May 8^th, 9^th, 15^th and 16^th  (9am – 1pm). You should attend all 4 sessions.

This is an advanced workshop which requires an intermediate level of R knowledge and experience. To participate in this workshop you must have either completed the Genomics Aotearoa Intermediate R workshop, or have an equivalent level of experience (e.g., be a semi-regular R user). Because of the complexity of this workshop we will not have the time or resources to solve coding errors. However, the focus of this workshop will be on the concepts and discussion of the statistical methodology rather than your ability to code quickly.

Because we expect a high level of interest in this workshop and we have limited spaces, we are inviting expressions of interest no later than Friday April 26^th and will select a group of attendees based on needs and experience. We will endeavour to maximise the overall positive impact on research in Aotearoa and distribute this training as fairly as possible. You will be advised whether you are able to attend the training by end of day Monday April 29^th. 

If we are not able to offer you a space in this training, you will be kept informed about future options for scRNA-seq training.

What will this workshop cover?

• Alignment and feature counting with Cell Ranger (briefly).
• QC and exploratory analysis.
• Normalisation.
• Sctransform: Variant Stabilising transformation.
• Feature selection and dimensionality reduction.
• Batch correction and data set integration.
• Clustering.
• Identification of cluster marker genes.
• Differential gene expression analysis.
• Differential abundance.

*Note that some of this material may be mentioned only briefly due to time constraints, in which case you will be pointed towards supplementary material for self-guided learning.

If you have any questions about this workshop, please contact Genomics Aotearoa Training Coordinator Dr Tyler McInnes (tyler.mcinnes@otago.ac.nz).

This workshop, taught by Professor Mik Black, will introduce skills and tools required for the analysis of single-cell RNA-seq data (scRNA-seq data) in R. The workshop will be taught online over four half-days, on May 8^th, 9^th, 15^th and 16^th  (9am – 1pm). You should attend all 4 sessions.

This is an advanced workshop which requires an intermediate level of R knowledge and experience. To participate in this workshop you must have either completed the Genomics Aotearoa Intermediate R workshop, or have an equivalent level of experience (e.g., be a semi-regular R user). Because of the complexity of this workshop we will not have the time or resources to solve coding errors. However, the focus of this workshop will be on the concepts and discussion of the statistical methodology rather than your ability to code quickly.

Because we expect a high level of interest in this workshop and we have limited spaces, we are inviting expressions of interest no later than Friday April 26^th and will select a group of attendees based on needs and experience. We will endeavour to maximise the overall positive impact on research in Aotearoa and distribute this training as fairly as possible. You will be advised whether you are able to attend the training by end of day Monday April 29^th. 

If we are not able to offer you a space in this training, you will be kept informed about future options for scRNA-seq training.

What will this workshop cover?

• Alignment and feature counting with Cell Ranger (briefly).
• QC and exploratory analysis.
• Normalisation.
• Sctransform: Variant Stabilising transformation.
• Feature selection and dimensionality reduction.
• Batch correction and data set integration.
• Clustering.
• Identification of cluster marker genes.
• Differential gene expression analysis.
• Differential abundance.

*Note that some of this material may be mentioned only briefly due to time constraints, in which case you will be pointed towards supplementary material for self-guided learning.

If you have any questions about this workshop, please contact Genomics Aotearoa Training Coordinator Dr Tyler McInnes (tyler.mcinnes@otago.ac.nz).

A reminder about this week’s Genomics Aotearoa seminar, online Friday, May 31 at 3pm.

We welcome Dafni Anastasiadi (Plant and Food Research). Dafni will be talking on Epigenetic clocks for age prediction.

Please invite colleagues to join our genomics community and take part in this seminar. Look forward to seeing you there. Questions and discussions are welcome.

Join from PC, Mac, iOS, or Android:
https://otago.zoom.us/j/97097442106?pwd=RlczU3VCdFBmbmt4Yng4VW5OcHdSdz09

About Dafni
Dafni Anastasiadi is a scientist at Plant and Food Research, Nelson. Her research interests focus on the role of epigenetics in eco-evolutionary processes using marine species as models. Her work has produced results with far-reaching implications in the epigenetics field, including the first epigenetic clock to accurately predict age in fish.

WORKSHOP: Reproducible Bioinformatics with Nextflow and nf-core
This online workshop is delivered by Genomics Aotearoa and NeSI, and will be taught from 10:00am to 4:00pm NZT on Wednesday the 5th of June, 2024, and is for New Zealand researchers interested in learning to use Nextflow.

Register for Reproducible Bioinformatics with Nextflow and nf-core

Nextflow is a management software system which facilitates the writing of scalable and reproducible scientific workflows. As a management system, Nextflow will simplify the development, monitoring, execution and sharing of pipelines. Using Nextflow will improve the reproducibility, portability, and run time of tasks.

Nextflow can integrate pipelines written in common scripting languages such as R and Python and couple these with environment management systems such as Docker, Singularity and Conda. Nextflow uses Domain Specific Language (DSL) which makes running workflows on cloud or high-performance computing (HPC) infrastructure easy.

This workshop will also introduce nf-core: a community-driven repository of peer-reviewed best practice analysis pipelines written in Nextflow.

This workshop is comprised of three sections:
Section 1
– An introduction to Nextflow.
– Useful terminology.
– Working in the Nextflow environment.
Section 2
– An introduction to nf-core – a repository of existing pipelines.
– General structure of a pipeline.
– Running and customising your first pipeline.
Section 3
– Customising and configuring pipelines.
– Metrics and shareable reports.

Setup
This is a fully online, hands-on workshop. This workshop material will be run on the NeSI OpenOnDemand training environment – there is no need to install any software for this workshop. Instructions on how to access the training platform will be sent out with the confirmation letter to registrants.
Participants must have their own laptops and plan to participate actively. You will require a working web browser.
Prerequisites: You must have basic command line (Bash) skills to participate in this workshop.
If you have any questions about these workshops, including whether they are suitable for you, please contact tyler.mcinnes@otago.ac.nz.