Browse or search for courses
Showing courses 126-136 of 136
Courses per page: 10 | 25 | 50 | 100
PLEASE NOTE The Bioinformatics Team are presently teaching as many courses live online, with tutors available to help you work through the course material on a personal copy of the course environment. We aim to simulate the classroom experience as closely as possible, with opportunities for one-to-one discussion with tutors and a focus on interactivity throughout.
This bootcamp provides an in depth look at statistical analyses using R.
Day 1 aims to introduce R as a tool for statistics and graphics, with the main aim being to become comfortable with the R environment. As well as introducing core R language concepts, this course also provides the basics of using the Tidyverse for data manipulation, and ggplot for plotting. It will focus on entering and manipulating data in R and producing simple graphs.
PLEASE NOTE: If you are already comfortable working in R and using the tidyverse package, you might find that you can skip Friday’s training session. Please review the pre-requisites section below for further information.
Day 2-6 (half days) will focus on the statistical possibilities of R, covering from experimental design to analysis of quantitative and qualitative data. Ample time will be given to participants to practise different type of analysis and interact with the trainers to discuss their statistical problems.
This event is organized in collaboration with the Babraham Institutes's Bioinformatics Group and it is supported by the BBSRC Strategic Training Awards for Research Skills (STARS) grant (BB/P022766/1).
Please note that if you are not eligible for a University of Cambridge Raven account you will need to book or register your interest by linking here.
Date | Availability | |
---|---|---|
Tue 25 Feb 2020 | 09:30 | Finished |
This course is intended to provide a strong foundation in practical statistics and data analysis using the R software environment. The underlying philosophy of the course is to treat statistics as a practical skill rather than as a theoretical subject and as such the course focuses on methods for addressing real-life issues in the biological sciences using the R software package.
In this course we explore classical statistical analysis techniques starting with simple hypothesis testing and building up to multiple linear regression. The focus of the course is on practical implementation of these techniques and developing robust statistical analysis skills rather than on the underlying statistical theory.
After the course you should feel confident to be able to select and implement common statistical techniques using R and moreover know when, and when not, to apply these techniques.
This event is supported by the BBSRC Strategic Training Awards for Research Skills (STARS) grant (BB/P022766/1).
The training room is located on the first floor and there is currently no wheelchair or level access available to this level.
Please note that if you are not eligible for a University of Cambridge Raven account you will need to book or register your interest by linking here.
Date | Availability | |
---|---|---|
Thu 21 Jun 2018 | 09:30 | Finished |
Mon 10 Sep 2018 | 09:30 | Finished |
Wed 9 Jan 2019 | 13:30 | Finished |
Wed 15 May 2019 | 09:30 | Finished |
This course aims to provide trainers with guidance and tips for developing and delivering training in image analysis, exploring a range of methods appropriate to different learning styles and examining the requirements for a successful course (both scientific and logistic).
The first part of the course will give participants principles of training theory and best practises for developing and delivering their future training content; the second part will be a hackathon to kick start the development of a common set of training materials in image analysis.
This event is organized in collaboration with the Image Analysis Focused Interest Group and is supported by the Royal Microscopical Society.
The training room is located on the first floor and there is currently no wheelchair or level access available to this level.
Please note that if you are not eligible for a University of Cambridge Raven account you will need to Book or register Interest by linking here.
Date | Availability | |
---|---|---|
Tue 10 May 2016 | 09:30 | Finished |
Mon 11 Jul 2016 | 09:30 | Finished |
Thu 25 Apr 2019 | 09:30 | Finished |
PLEASE NOTE The Bioinformatics Team are presently teaching as many courses live online, with tutors available to help you work through the course material on a personal copy of the course environment. We aim to simulate the classroom experience as closely as possible, with opportunities for one-to-one discussion with tutors and a focus on interactivity throughout.
RNA-Seq technology has been transformative in our ability to explore gene content and gene expression in all realms of biology, and de novo transcriptome assembly has enabled opportunities to expand transcriptome analysis to non-model organisms.
This course provides an overview of modern applications of transcriptome sequencing and popular tools, and algorithms, for exploring transcript reconstruction and expression analysis in a genome-free manner.
Attendees will perform quality assessment and upstream analysis of both Illumina and long reads single molecule sequencing data; the derived transcriptomes will be compared, annotated and used as reference for quantifying transcript expression, leveraging on Bioconductor tools for differential expression analysis. Additional methods will be explored for characterising the assembled transcriptome and revealing biological findings.
Please note that if you are not eligible for a University of Cambridge Raven account you will need to book or register your interest by linking here.
Date | Availability | |
---|---|---|
Mon 15 Apr 2019 | 09:30 | Finished |
Microscopy experiments have proven to be a powerful means of generating information-rich data for biological applications. From small-scale microscopy experiments to time-lapse movies and high-throughput screens, automatic image analysis is more objective and quantitative and less tedious than visual inspection.
This course will introduce users to the free open-source image analysis program CellProfiler and its companion data exploration program CellProfiler Analyst. We will show how CellProfiler can be used to analyse a variety of types of imaging experiments. We will also briefly discuss the basic principles of supervised machine learning with CellProfiler Analyst in order to score complex and subtle phenotypes.
The training room is located on the first floor and there is currently no wheelchair or level access available to this level.
Please note that if you are not eligible for a University of Cambridge Raven account you will need to book or register your interest by linking here.
Date | Availability | |
---|---|---|
Thu 15 Dec 2016 | 09:30 | Finished |
Wed 13 Dec 2017 | 09:30 | Finished |
Mon 10 Dec 2018 | 09:30 | Finished |
The Ensembl Project provides an interface and an infrastructure for accessing genomic information, including genes, variants, comparative genomics and gene regulation data, covering over 300 vertebrate species. This workshop offers a comprehensive practical introduction to the use of the Ensembl genome browser as well as essential background information.
This course will focus on the vertebrate genomes in Ensembl, however much of what will be covered is also applicable to the non-vertebrates (plants, bacteria, fungi, metazoa and protists) in Ensembl Genomes.
If you do not have a University of Cambridge Raven account please book or register your interest here.
- Our courses are only free for registered University of Cambridge students. All other participants will be charged according to our charging policy.
- Attendance will be taken on all courses and a charge is applied for non-attendance, including for University of Cambridge students. After you have booked a place, if you are unable to attend any of the live sessions, please email the Bioinfo Team.
- Further details regarding eligibility criteria are available here.
Date | Availability | |
---|---|---|
Mon 23 Mar 2015 | 09:30 | Finished |
Mon 22 Jun 2015 | 09:30 | Finished |
Fri 27 Nov 2015 | 09:30 | Finished |
Mon 14 Mar 2016 | 09:30 | Finished |
Thu 9 Jun 2016 | 14:00 | Finished |
Tue 20 Sep 2016 | 09:30 | Finished |
Fri 3 Mar 2017 | 09:30 | Finished |
Tue 2 May 2017 | 09:30 | Finished |
Fri 8 Sep 2017 | 09:30 | Finished |
Mon 12 Mar 2018 | 09:30 | Finished |
Fri 20 Jul 2018 | 09:30 | Finished |
Mon 12 Nov 2018 | 09:30 | Finished |
Wed 10 Apr 2019 | 09:30 | Finished |
Wed 27 Nov 2019 | 09:30 | Finished |
Tue 1 Sep 2020 | 09:30 | Finished |
Thu 11 Feb 2021 | 09:30 | Finished |
Thu 30 Sep 2021 | 09:30 | Finished |
Mon 14 Feb 2022 | 09:30 | Finished |
Thu 15 Sep 2022 | 09:30 | CANCELLED |
Thu 8 Dec 2022 | 09:30 | Finished |
This workshop will focus on the core steps involved in calling variants with the Broad’s Genome Analysis Toolkit, using the “Best Practices” developed by the GATK team. You will learn why each step is essential to the variant discovery process, what are the operations performed on the data at each step, and how to use the GATK tools to get the most accurate and reliable results out of your dataset.
In the course of this workshop, we highlight key functionalities such as the germline GVCF workflow for joint variant discovery in cohorts, RNAseq specific processing, and somatic variant discovery using MuTect2. We also preview capabilities of the upcoming GATK version 4, including a new workflow for CNV discovery, and we demonstrate the use of pipelining tools to assemble and execute GATK workflows.
The workshop is composed of one day of lectures and two days of handson training, structured as follows. Day 1: theory and application of the Best Practices for Variant Discovery in highthroughput sequencing data. Day 2 and the morning of Day 3: handson exercises on how to manipulate the standard data formats involved in variant discovery and how to apply GATK tools appropriately to various use cases and data types. Day 3 afternoon: hands-on exercises on how to write workflow scripts using WDL, the Broad's new Workflow Description Language, and to execute these workflows locally as well as through a publicly accessible cloud-based service.
Please note that this workshop is focused on human data analysis. The majority of the materials presented does apply equally to nonhuman data, and we will address some questions regarding adaptations that are needed for analysis of non-human data, but we will not go into much detail on those points.
Please note that if you are not eligible for a University of Cambridge Raven account you will need to Book or register Interest by linking here.
Date | Availability | |
---|---|---|
Thu 23 Apr 2015 | 09:30 | Finished |
Mon 13 Jun 2016 | 09:30 | Finished |
This workshop will focus on the core steps involved in calling variants from Illumina next generation sequencing data using the Genome Analysis Toolkit (GATK). You will learn about best practices in calling somatic variants: single nucleotide variants (SNVs), short insertion/deletions (indels) and copy number variants (CNVs). We will also cover considerations to take when calling variants on the mitochondrial genome, as well as variant calling from bulk and single-cell RNA-seq data. We will also cover how the data structures provided by GATK can help you process large datasets in parallel and at scale. Although this workshop focuses on human data, the majority of the concepts and approaches apply to non-human data, and we will cover some adaptations needed in those situations.
The training room is located on the first floor and there is currently no wheelchair or level access available to this level.
Please note that if you are not eligible for a University of Cambridge Raven account you will need to Book or register Interest by linking here.
Date | Availability | |
---|---|---|
Mon 16 Jul 2018 | 09:30 | Finished |
Mon 8 Jul 2019 | 09:30 | Finished |
This course covers state-of-the-art tools and methods for NGS RNA-seq and exome variant data analysis, which are of major relevance in today's genomic and gene expression studies.
It is oriented to experimental researchers, post-doctoral and PhD students who want to learn about the state-of-the-art of genomic variant and transcriptomics data analysis methodologies and carry out their own analysis.
Further information is available here.
Please note that if you are not eligible for a University of Cambridge Raven account you will need to book by linking here.
Date | Availability | |
---|---|---|
Mon 23 Feb 2015 | 09:30 | Finished |
This comprehensive course equips you with essential skills and knowledge in bacterial genomics analysis, primarily using Illumina-sequenced samples. You'll gain an understanding of how to select the most appropriate analysis workflow, tailored to the genome diversity of a given bacterial species. Through hands-on training, you'll apply both de novo assembly and reference-based mapping approaches to obtain bacterial genomes for your isolates. You will apply standardised workflows for genome assembly and annotation, including quality assessment criteria to ensure the reliability of your results. Along with typing bacteria using methods such as MLST, you'll learn how to construct phylogenetic trees using whole genome and core genome alignments, enabling you to explore the evolutionary relationships among bacterial isolates. You’ll extend this to estimate a time-scaled phylogeny using a starting phylogenetic tree. Lastly, you'll apply methods to detect antimicrobial resistance genes. As examples we will use Mycobacterium tuberculosis, Staphylococcus aureus and Streptococcus pneumoniae, allowing you to become well-equipped to conduct bacterial genomics analyses on a range of species.
If you do not have a University of Cambridge Raven account please book or register your interest here.
- ♿ The training room is located on the first floor and there is currently no wheelchair or level access.
- Our courses are only free for registered University of Cambridge students. All other participants will be charged according to our charging policy.
- Attendance will be taken on all courses and a charge is applied for non-attendance, including for University of Cambridge students. After you have booked a place, if you are unable to attend any of the live sessions, please email the Bioinfo Team.
- Further details regarding eligibility criteria are available here.
Date | Availability | |
---|---|---|
Mon 11 Dec 2023 | 09:30 | Finished |
This course will cover concepts and strategies for working more effectively with Python with the aim of writing reusable code. In the morning session, we will briefly go over the basic syntax, data structures and control statements. This will be followed by an introduction to writing user-defined functions. We will finish the course by looking into how to incorporate existing python modules and packages into your programs as well as writing you own modules.
Course materials can be found here.
Note: this one-day course is the continuation of the Introduction to Solving Biological Problems with Python; participants are expected to have attended the introductory Python course and/or have acquired some working knowledge of Python. This course is also open to Python beginners who are already fluent in other programming languages as this will help them to quickly get started in Python.
Please note that if you are not eligible for a University of Cambridge Raven account you will need to book by linking here.
Date | Availability | |
---|---|---|
Mon 27 Mar 2017 | 09:30 | Finished |
Fri 28 Apr 2017 | 09:30 | Finished |
Wed 21 Jun 2017 | 09:30 | Finished |
Thu 12 Oct 2017 | 09:30 | Finished |
Wed 6 Dec 2017 | 09:30 | Finished |
Thu 5 Apr 2018 | 09:30 | POSTPONED |
Thu 3 May 2018 | 09:30 | Finished |
Thu 31 May 2018 | 09:30 | POSTPONED |