Browse or search for courses
Showing courses 1-10 of 136
Courses per page: 10 | 25 | 50 | 100
In this course you will acquire practical skills in RNA-seq data analysis. You will learn about quality control, alignment, and quantification of gene expression against a reference transcriptome. Additionally, you will learn to conduct downstream analysis in R, exploring techniques like PCA and clustering for exploratory analysis. The course also covers differential expression analysis using the DESeq2 R/Bioconductor package. Furthermore, the course covers how to generate visualisations like heatmaps and performing gene set testing to link differential genes with established biological functions or pathways.
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.
- Guidance on visiting Cambridge and finding accommodation is available here.
Date | Availability | |
---|---|---|
Mon 18 Jun 2018 | 09:30 | Finished |
Mon 3 Sep 2018 | 09:30 | Finished |
Wed 27 Mar 2019 | 09:30 | Finished |
Mon 2 Sep 2019 | 09:30 | Finished |
Tue 19 May 2020 | 09:30 | Finished |
Wed 1 Jul 2020 | 09:30 | Finished |
Wed 18 Nov 2020 | 09:30 | Finished |
Mon 22 Mar 2021 | 09:30 | Finished |
Wed 21 Apr 2021 | 09:30 | Finished |
Wed 30 Jun 2021 | 09:30 | Finished |
Mon 15 Nov 2021 | 09:30 | Finished |
Thu 17 Feb 2022 | 09:30 | Finished |
Thu 28 Apr 2022 | 09:30 | Finished |
Fri 18 Nov 2022 | 09:30 | Finished |
Fri 17 Mar 2023 | 09:30 | Finished |
Fri 17 Mar 2023 | 09:30 | Finished |
Fri 23 Jun 2023 | 09:30 | Finished |
Fri 23 Jun 2023 | 09:30 | Finished |
Fri 17 Nov 2023 | 09:30 | Finished |
Fri 15 Mar 2024 | 09:30 | Finished |
Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is a method used to identify binding sites for transcription factors, histone modifications and other DNA-binding proteins across the genome. In this course, we will cover the fundamentals of ChIP-seq data analysis, from raw data to downstream applications.
We will start with an introduction to ChIP-seq methods and cover the bioinformatic steps in processing ChIP-seq data. We will then introduce the use of the graphical program SeqMonk to explore and visualise your data. Finally, you will perform peak calling and perform differential enrichment analysis.
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.
- Guidance on visiting Cambridge and finding accommodation is available here.
This course will cover all aspects of the analysis of DNA methylation using sequencing, including primary analysis, mapping and quality control of BS-Seq data, common pitfalls and complications.
It will also include exploratory analysis of methylation, looking at different methods of quantitation, and a variety of ways of looking more widely at the distribution of methylation over the genome. Finally the course will look at statistical methods to predict differential methylation.
The course comprises of a mixture of theoretical lectures and practicals covering a range of different software packages.
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.
- Guidance on visiting Cambridge and finding accommodation is available here.
Date | Availability | |
---|---|---|
Fri 24 Jul 2015 | 09:30 | Finished |
Wed 8 Jun 2016 | 09:30 | Finished |
Fri 2 Dec 2016 | 09:30 | Finished |
Wed 14 Jun 2017 | 09:30 | Finished |
Wed 15 Nov 2017 | 09:30 | Finished |
Wed 27 Jun 2018 | 09:30 | Finished |
Fri 14 Dec 2018 | 09:30 | Finished |
Wed 20 Nov 2019 | 09:30 | Finished |
Fri 16 Oct 2020 | 09:30 | Finished |
Fri 7 May 2021 | 09:30 | Finished |
This workshop focuses on expression proteomics, which aims to characterise the protein diversity and abundance in a particular system. You will learn about the bioinformatic analysis steps involved when working with these kind of data, in particular several dedicated proteomics Bioconductor packages, part of the R programming language. We will use real-world datasets obtained from label free quantitation (LFQ) as well as tandem mass tag (TMT) mass spectrometry. We cover the basic data structures used to store and manipulate protein abundance data, how to do quality control and filtering of the data, as well as several visualisations. Finally, we include statistical analysis of differential abundance across sample groups (e.g. control vs. treated) and further evaluation and biological interpretation of the results via gene ontology analysis. By the end of this workshop you should have the skills to make sense of expression proteomics data, from start to finish.
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.
- Guidance on visiting Cambridge and finding accommodation is available here.
Date | Availability | |
---|---|---|
Thu 24 Jan 2019 | 09:30 | Finished |
Tue 5 Dec 2023 | 09:30 | Finished |
This advanced course will cover high-throughput sequencing data processing, ChIP-seq data analysis (including alignment, peak calling), differences in analyses methods for transcription factors (TF) binding and epigenomic datasets, a range of downstream analysis methods for extracting meaningful biology from ChIP-seq data and will provide an introduction to the analysis of open chromatin with ATAC-seq and long-distance interactions with chromosomal conformation capture based Hi-C datasets.
Materials for this course can be found here.
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.
This course provides an introduction to the tools available through the Bioconductor project for manipulating and analysing high-throughput sequencing (HTS) data. We will present workflows for the analysis of ChIP-Seq and RNA-seq data starting from aligned reads in bam format. We will also describe the various resources available through Bioconductor to annotate and visualize HTS data, which can be applied to any type of sequencing experiment.
The course timetable 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 1 Jun 2015 | 09:30 | Finished |
Mon 30 Nov 2015 | 09:30 | Finished |
PLEASE NOTE that until further notice, due to the evolving situation with Coronavirus no courses will be offered as classroom based at the Training Facility. The Bioinformatics Team will be teaching the course live online in conjunction with the presenters.
SeqMonk is a graphical program for the visualisation and analysis of large mapped sequencing datasets such as ChIP-Seq, RNA-Seq, and BS-Seq.
The program allows you to view your reads against an annotated genome and to quantitate and filter your data to let you identify regions of interest. It is a friendly way to explore and analysis very large datasets.
This course provides an introduction to the main features of SeqMonk and will run through the analysis of a couple of different datasets to show what sort of analysis options it provides.
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 or register your interest by linking here.
Date | Availability | |
---|---|---|
Fri 13 Mar 2015 | 09:30 | Finished |
Wed 19 Aug 2015 | 09:30 | Finished |
Wed 3 Feb 2016 | 09:30 | Finished |
This course provides an introduction to the tools available through the Bioconductor project for manipulating and analysing bulk RNA-seq data. We will present a workflow for the analysis RNA-seq data starting from aligned reads in bam format and producing a list of differentially-expressed genes. We will also describe the various resources available through Bioconductor to annotate, visualise and gain biological insight from the differential expression results.
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 | |
---|---|---|
Thu 4 May 2017 | 09:30 | Finished |
Recent technological advances have made it possible to obtain genome-wide transcriptome data from single cells using high-throughput sequencing (scRNA-seq). Even though scRNA-seq makes it possible to address problems that are intractable with bulk RNA-seq data, analysing scRNA-seq is also more challenging.
In this course we will be surveying the existing problems as well as the available computational and statistical frameworks available for the analysis of scRNA-seq.
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.
- Guidance on visiting Cambridge and finding accommodation is available here.
Date | Availability | |
---|---|---|
Wed 24 Feb 2016 | 09:30 | Finished |
Wed 22 Jun 2016 | 09:30 | Finished |
Wed 26 Oct 2016 | 09:30 | Finished |
Thu 16 Mar 2017 | 09:30 | Finished |
Tue 31 Oct 2017 | 09:30 | Finished |
Thu 23 May 2019 | 09:30 | Finished |
Mon 16 Dec 2019 | 09:30 | Finished |
Thu 4 Nov 2021 | 09:30 | Finished |
Fri 4 Feb 2022 | 09:30 | Finished |
Fri 17 Jun 2022 | 09:30 | Finished |
Mon 12 Sep 2022 | 09:30 | Finished |
Wed 18 Jan 2023 | 09:30 | Finished |
Thu 18 May 2023 | 09:30 | Finished |
Wed 27 Sep 2023 | 09:30 | Finished |
Fri 19 Jan 2024 | 09:30 | Finished |
This course focuses on methods for the analysis of small non-coding RNA data obtained from high-throughput sequencing (HTS) applications (small RNA-seq). During the course, approaches to the investigation of all classes of small non-coding RNAs will be presented, in all organisms.
Day 1 will focus on the analysis of microRNAs and day 2 will cover the analysis of other types of small RNAs, including Piwi-interacting (piRNA), small interfering (siRNA), small nucleolar (snoRNA) and tRNA-derived (tsRNA).
Please note that if you are not eligible for a University of Cambridge Raven account you will need to book by linking here.