Welcome to Epigenomics Workshop Test Page!¶
Online workshop open for PhD students, postdocs, researchers and other employees within Swedish academia. This course is organised by the National Bioinformatics Infrastructure Sweden (NBIS).
This workshop builds on our previous ChIPseq data analysis workshop to introduce best practice bioinformatics methods for processing, analyses and integration of epigenomics data. The online teaching includes lectures, programming tutorials and interactive group sessions.
Important dates¶
Application opens: August, 1st, 2020
Application deadline: November, 1st, 2020
Confirmation to accepted students: November, 7th, 2020
Course days: 23rd - 27th, November, 2020
Workshop content¶
This workshop is designed to introduce best practice bioinformatics methods for processing, analyses and integration of epigenomics and functional genomics data.
Topis covered include:
Data processing and analyses for differential DNA methylation with Illumina EPIC arrays and Bisulfite-seq;
ChIP-seq and ATAC-seq: peak calling, peak independent / dependent quality metrics, differential binding and differential accessibility analysis; DNA motif enrichment;
Functional analysis, including finding nearest genes and custom features, GO terms and Reactome pathways enrichment;
Integrative visualisations of epigenomics datasets;
RNA-seq integration for identification of targets of transcription factors;
Basic multi-omics exploration and integration;
Introduction to analysis of single cell functional genomics data (ATAC-seq);
Nf-cores pipelines: Methylseq, ChIP-seq, ATAC-seq
Entry requirements¶
Required to be able to follow the tutorials:
BYOL, bring your own laptop with R and RStudio installed
Basic knowledge in Linux
Basic R programming experience
Makes learning experience easier:
Experience working on the SNIC center Uppmax or another HPC
Previous experience with NGS data analyses
Completing NBIS workshops “Introduction to Bioinformatics using NGS data” and “R Programming Foundations for Life Scientists” or equivalent
Application¶
Application is now open [here](https://forms.gle/zBorhLmT3ZNBn7bm8).
Application deadline: 1st November, 2020
Selection criteria¶
Due to limited capacity the workshop can accommodate maximum of 30 participants. If we receive more applications, participants will be selected based on several criteria. Selection criteria include correct entry requirements, motivation to attend the course as well as gender and geographical balance.
NBIS prioritises academic participants, especially PhD students, affiliated with Swedish universities. We warmly welcome international and/or non-academic participants when we have seats available and the requirements criteria are met.
Certificate & University credits¶
We will issue a course certificate upon a successful course completion, assessed by active participation in all course sessions (lectures, computer practicals, group discussion etc.).
Unfortunately we are not able to warrant any university credits (högskolepoäng). Many universities however, recognize the attendance in our courses and award 1.5 HPs, corresponding to a 40 h of studying. It is up to participants to clarify and arrange credit transfer with the relevant university department.
Teaching team¶
Phil Ewels <phil.ewels@scilifelab.se>