Pinned Repositories
2020-berlin-python-course
2022-berlin-python-course
2023-berlin-python-course
convert-spread3
A horrible shell script hack to convert SpreadD3 output files for Christian
csd3-pipeline
A SLURM pipeline to run on the Cambridge CSD3 cluster
gb2seq
Use a GenBank file to extract sequences for features and other information from another genome
python-testing-course-2022
Notes from an intro course on testing in Python
SARS-CoV-2-VL-paper
Data and files from the May 25, 2021 SARS-CoV-2 viral load and infectiousness paper
sars2seq
A Python library and command-line scripts for working with SARS-CoV-2 sequences
valencia-gb2seq-talk
Talk by Terry for the 2023 International Virus Bioinformatics Meeting
Institute of Virology, Charité, Berlin's Repositories
VirologyCharite/SARS-CoV-2-VL-paper
Data and files from the May 25, 2021 SARS-CoV-2 viral load and infectiousness paper
VirologyCharite/gb2seq
Use a GenBank file to extract sequences for features and other information from another genome
VirologyCharite/convert-spread3
A horrible shell script hack to convert SpreadD3 output files for Christian
VirologyCharite/python-testing-course-2022
Notes from an intro course on testing in Python
VirologyCharite/2020-berlin-python-course
VirologyCharite/2022-berlin-python-course
VirologyCharite/sars2seq
A Python library and command-line scripts for working with SARS-CoV-2 sequences
VirologyCharite/valencia-gb2seq-talk
Talk by Terry for the 2023 International Virus Bioinformatics Meeting
VirologyCharite/2023-berlin-python-course
VirologyCharite/2024-berlin-python-course
VirologyCharite/csd3-pipeline
A SLURM pipeline to run on the Cambridge CSD3 cluster
VirologyCharite/baxolele-stop-codons
Counting stop codons at a certain location in a BAM file for Baxolele
VirologyCharite/minor-variants
VirologyCharite/2019-berlin-python-course
VirologyCharite/2021-berlin-python-course
The 2021 Berlin Python course, of course
VirologyCharite/antigenic-cartography-introduction-hu
VirologyCharite/bih-env
Shared shell environment setup for the civ-diagnostics group on the BIH cluster
VirologyCharite/bioconda-recipes
Conda recipes for the bioconda channel.
VirologyCharite/bowtie2-bam-input
Trying to get the -b option to bowtie2 to work
VirologyCharite/charite-hamster-map-2024
Data and code for "Antigenic cartography using variant-specific hamster sera reveals substantial antigenic variation among Omicron subvariants"
VirologyCharite/ConsensusDeduplication
consensus-deduplication repo duplicate without history
VirologyCharite/diamond-sensitivity
VirologyCharite/Fabian-SNP-analysis
VirologyCharite/firewall
Script to automate requests to open up the wired firewall
VirologyCharite/jules-mutation-plots
VirologyCharite/make-tables-with-code
Making tables with code
VirologyCharite/python-line-counting
Scripts for counting non-blank non-comment lines in Python and Jupyter notebook files
VirologyCharite/Sam_to_Fragmentsize
For NGS reads mapped to a reference, how big were the fragments from which these reads were generated?
VirologyCharite/sars-cov-2-agrdt-study
Code and partial data for manuscript "SARS-CoV-2 rapid antigen test sensitivity and viral load in freshly symptomatic hospital employees in Berlin, Germany, December 2020 to February 2022 - an observational study".
VirologyCharite/terry-jones-2020-hannover-lectures
Class materials from Terry Jones Feb 13th computational virology lectures in Hannover