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DTSTAMP:20260808T230103Z
UID:5decfc4c-8b8d-4237-87d9-2f3ab5ae3a7e
DTSTART:20240729T070000Z
DTEND:20240812T150000Z
DESCRIPTION:Educators:\nFabian Müller\nJörn Walter (HD-HuB)\nSaarbrücken
  de.NBI team (HD-HuB)\n\nDate: \nJuly 29 – August 12 \n\nLocation: \nUni
 versität des Saarlandes\n\nOutline:\nThis workshop offers an introduction
  into bioinformatics methods and tools for integrated NGS-based (NGS = nex
 t-generation sequencing) epigenome analysis. The course starts with two le
 cturing days introducing/refreshing participants' knowledge of epigenetic 
 gene regulation and introduces a series of experimental methods to profile
  the epigenome. You will then delve into the theoretical background of bio
 informatics methods and software tools used for data processing. You learn
  about quality control methods\, exploratory analyses\, differential analy
 ses\, and integration of multiple data modalities. Four epigenomic data mo
 dalities will be analysed in detail: gene expression\, DNA methylation\, c
 hromatin accessibility\, and histone modifications. The theoretical knowle
 dge conveyed in the lectures will then be solidified in a four day hands-o
 n workshop\, in which the participants in groups of 2 will employ the intr
 oduced methods. \n\nParticipants should be familiar and trained in the use
  of UNIX shell and R. To make them familiar with the working environment a
 ll participants are obliged to successfully participate in a Data Camp tut
 orial provided before the course starts. \n\nContent:\nPrecourse work:\n- 
 Exercises in UNIX shell and R usage via a DataCamp module.\nLectures follo
 wed by practical exercises:\n- Introduction into principles of epigenetic 
 gene regulation.\n- Experimental techniques and bioinformatic analysis for
  gene expression (RNA-seq).\n- Experimental techniques and bioinformatic a
 nalysis for DNA methylation (WGBS/Bisulfiteseq\, microarrays\, enrichment-
 based methods\, etc.).\n- Experimental techniques and bioinformatic analys
 is for chromatin accessibility (ATAC-seq\, DNase-seq\, NOMe-seq\, etc.).\n
 - Experimental techniques and bioinformatic analysis for histone modificat
 ions (ChIP-seq\, CUT&amp\;RUN\, etc.).\n- Integrative data analysis: Dimen
 sion reduction\, clustering\, differential analysis\, segmentation\, imput
 ation.\n- Emerging epigenome profiling technologies (including single-cell
  and multiome methods).\n\nSchedule\n- April 29 to July 28 (self-guided): 
 (Re-)Familiarize yourselves with the UNIX shell and R programming in the D
 ataCamp classroom and complete the mandatory courses - Online.\n- July 29 
 to 31: Six theoretical lectures (90 minutes each) introducing the biologic
 al and bioinformatics background (Can be attended online).\n- August 5 -9 
 (9am – 5pm): Hands-on workshop (in presence).\n- August 12: Presentation
  of results. (Mandatory for participants who aim to obtain full credit poi
 nts for the course. (in presence) \n\nAdmission:\nTo enroll\, participants
  should have a basic knowledge of modern genomics and epigenetics. Basic s
 kills for script-based programming using the R language and the use of UNI
 X is mandatory. Participants will have the opportunity to (re-)familiarize
  themselves using a DataCamp classroom provided upon registration. In this
  DataCamp mandatory courses on UNIX shell usage and R scripting will have 
 to be completed in the DataCamp classroom before the lecture of the worksh
 op starts (i.e.\, by July 28\, 2024). The course will be limited to up to 
 10 external participants. Non-bioinformatics participants will be accepted
  on an individual basis if they can demonstrate that the bioinformatic req
 uirements are met. Certificate(s) To obtain a certificate of participation
  participants have to: 1. Successfully participate in the introductory cou
 rse on DataCamp. 2. Fully attend all lectures (online) and the course (in 
 person) To obtain a qualified certificate of participation (5 Credit Point
 s) participants need to: 1. Complete the introductory course on DataCamp. 
 2. Pass the test on lectures. 3. Hand in a notebook-based (R Markdown) pro
 tocol. 4. Give a final presentation (n person). \n\nLearning Goals: \n- Un
 derstand the bioinformatics processing of DNA methylation\, histone modifi
 cations\, gene expression\, and chromatin accessibility.\n- Prepare and de
 scribe raw read files.\n- Evaluate NGS data.\n- Understand the individual 
 role of each assay-specific data.\n- Learn how to integrate various modali
 ties and how to decipher the cross-talk between various epigenomic modific
 ations. \n\nPrerequisites: \nThe course requires basic skills in:\n- Linux
 /bash\n- R \n\nKeywords: \nDNA methylation\, histone modifications\, RNA-S
 eq\, ATAC-Seq\, integrative analysis\, dimension reduction\, clustering\, 
 differential analysis\, segmentation\, imputation. \n\nTools: \nnf-core\, 
 conda\, singularity\, RnBeads\, methylSeekR\, chromHMM\, ChrAccR\, edgeR\,
  deeptools.
LOCATION:Saarbrücken
SUMMARY:Computational Methods for Epigenome Analysis
URL;VALUE=URI:https://www.denbi.de/training-courses-2024/1722-computational
 -methods-for-epigenome-analysis
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