MaximilianStammnitz
Geneticist. Exploring contagious cancer cells and Tasmanian devil conservation through bioinformatics. @DevilsAdvoMax
University of CambridgeCambridge, U.K.
Pinned Repositories
Indelwald
R processing of indels.
MSG
Wrapper for processing of rearrangement calls.
puntseq
PuntSeq - Chasing the microbial diversity of Cambridge's freshwater
RetroSeq
RetroSeq is a bioinformatics tool that searches for mobile element insertions from aligned reads in a BAM file and a library of reference transposable elements. Please read the wiki page (link below) for usage instructions. Also, there is a page on the wiki describing how the 1000 genomes CEU trio was carried out with the files and parameters used for the various steps.
scanPAV
Pipeline to detect PAVs (presence/absence variations) in genome comparison using whole genome alignment.
somatypus
A Platypus-based variant calling pipeline for cancer data
SubstitutionSafari
R processing of substitutions.
TCG2023
Companion scripts for data processing in Stammnitz et al., 2023
The-origins-and-vulnerabilities-of-two-transmissible-cancers-in-Tasmanian-devils
Analyses for "The origins and vulnerabilities of two transmissible cancers in Tasmanian devils". Cancer Cell 33(4), 607-619 (2018).
turtle-FP-cancer
Copy number analysis for Yetsko, Farrell et al., 2020
MaximilianStammnitz's Repositories
MaximilianStammnitz/Indelwald
R processing of indels.
MaximilianStammnitz/SubstitutionSafari
R processing of substitutions.
MaximilianStammnitz/MSG
Wrapper for processing of rearrangement calls.
MaximilianStammnitz/puntseq
PuntSeq - Chasing the microbial diversity of Cambridge's freshwater
MaximilianStammnitz/RetroSeq
RetroSeq is a bioinformatics tool that searches for mobile element insertions from aligned reads in a BAM file and a library of reference transposable elements. Please read the wiki page (link below) for usage instructions. Also, there is a page on the wiki describing how the 1000 genomes CEU trio was carried out with the files and parameters used for the various steps.
MaximilianStammnitz/scanPAV
Pipeline to detect PAVs (presence/absence variations) in genome comparison using whole genome alignment.
MaximilianStammnitz/somatypus
A Platypus-based variant calling pipeline for cancer data
MaximilianStammnitz/TCG2023
Companion scripts for data processing in Stammnitz et al., 2023
MaximilianStammnitz/The-origins-and-vulnerabilities-of-two-transmissible-cancers-in-Tasmanian-devils
Analyses for "The origins and vulnerabilities of two transmissible cancers in Tasmanian devils". Cancer Cell 33(4), 607-619 (2018).
MaximilianStammnitz/turtle-FP-cancer
Copy number analysis for Yetsko, Farrell et al., 2020
MaximilianStammnitz/svimmer
Structural variant merging tool
MaximilianStammnitz/TCG2019
Scripts accompanying publication Baez-Ortega et al., 2019
MaximilianStammnitz/webpage
Testing my mini-webpage