Epigenomics gene regulations

Short talk: PoDCall - Positive droplet calling and normalization of droplet digital PCR methylation data

PoDCall - Positive droplet calling and normalization of droplet digital PCR methylation data Marine Jeanmougin,Hans Petter Brodal,Heidi Pharo,Guro Elisabeth Lind Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital Abstract Droplet digital PCR (ddPCR) is an attractive technology for analyses of DNA methylation. ddPCR consists in partitioning samples into droplets, each undergoing its own PCR amplification. At end-point reactions, the droplets containing the fluorescent PCR target molecule are scored as (i) “positive”, and used to estimate the target concentration in the sample from binomial Poisson statistics, or (ii) “negative”, if they don’t contain the target of interest.

Short talk: Large-scale analyses of biological sequence motifs with the universalmotif package

Large-scale analyses of biological sequence motifs with the universalmotif package Benjamin JM Tremblay Centre for Research in Agricultural Genomics (CRAG), CSIC‐IRTA‐UAB‐UB, Spain Abstract Motifs are a common way of representing patterns in biological sequences, such as transcription factor binding sites or specific protein active sites. Predicting the presence or absence of these patterns within sequences is a crucial step in understanding their regulation or function. Additionally, determining the similarity or distance between motifs can help in identifying duplicate motifs and comparing motif evolution with function.

Short talk: iCLIP data analysis: Defining binding sites, an R package

iCLIP data analysis: Defining binding sites, an R package Mirko Brüggemann Goethe University Frankfurt Abstract Most cellular processes are regulated by RNA-binding proteins (RBPs). Knowledge on their exact positioning can be obtained from individual-nucleotide resolution UV crosslinking and immunoprecipitation (iCLIP) experiments. In a recent publication we described a complete analysis workflow to detect RBP binding sites from iCLIP data. The workflow covers all essential steps, from quality control of sequencing reads, different peak calling options, to the downstream analysis and definition of binding sites.

Short talk: CLIPflexR: a generic R package for CLIP analysis

CLIPflexR: a generic R package for CLIP analysis Kathryn Rozen-Gagnon The Rockefeller University Abstract By now, transcriptome-wide maps of RNA binding protein (RBP) target sites or RNA modifications are routinely generated via crosslinking immunoprecipitation followed by high-throughput sequencing (CLIP-seq). While CLIP-seq is a common approach to understand post-transcriptional RNA networks, researchers still face considerable obstacles in subsequent bioinformatic analyses. First, computational set-ups are laborious due to disparate workflows requiring multiple dependencies.