Name: Charlotte Capitanchik
Type: User
Bio: Postgraduate Research Associate at UK DRI King's College London. Previously, PhD student in RNA biology @ Francis Crick Institute, London.
Twitter: tiny_captain
Location: London
Blog: https://charlotteannecap.wixsite.com/mysite
Charlotte Capitanchik's Projects
Conda recipes for the bioconda channel.
CLIP sequencing analysis pipeline for QC, pre-mapping, genome mapping, UMI deduplication, and multiple peak-calling options.
:books: Product documentation template for Jekyll
nextflow pipeline to get fastas
LaBranchoR predicts RNA splicing branchpoints using a LSTM network. LaBranchoR uses only the sequence 1 to 70 base pairs upstream of a three prime splice site as a feature. In our paper, we show that LaBranchoR predicts a correct branchpoint for over 90% of 3' splice sites! See our website for precomputed predictions for all introns in gencode v19.
Repository to host tool-specific module files for the Nextflow DSL2 community!
A collection of scripts for my Bioinformatics MSc thesis
After duplex calling using Guppy you are left with a fastq of duplexes and one of simplexes - this script takes both and the list of paired reads to create one final file where there is not duplication of reads.
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
Test data to be used for automated testing with the nf-core pipelines
Accelerating the deduplication and collapsing process for reads with Unique Molecular Identifiers (UMI). Heavily optimized for scalability and orders of magnitude faster than a previous tool.