Areeba Patel's repositories
Aeron
Alignment, quantification and fusion prediction from long RNA reads
chimeraviz
chimeraviz is an R package that automates the creation of chimeric RNA visualizations.
CLAM
Data-efficient and weakly supervised computational pathology on whole slide images - Nature Biomedical Engineering
hap.py
Haplotype VCF comparison tools
humanunsupervised.com
Machine learning Jupyter notebooks, tutorials, and code
mosdepth
fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing
PyMethylProcess
Preprocessing methylation pipeline, written in python. Easy to use and highly parallelized.
Rapid-CNS2
Rapid comprehensive adaptive nanopore-sequencing of CNS tumours set-up and analysis pipeline
Rapid-CNS2_sh
Neuropathology Heidelberg Rapid-CNS2 pipeline (bash + docker)
readfish
Read Until scripts
sicelore
Single Cell Long Read is a suite of tools dedicated to Cell barcode / UMI assignment and analysis of highly multiplexed single cell Nanopore long read sequencing data.
smCounter
smCounter: a versatile UMI-aware variant caller to detect both somatic and germline SNVs and indels. Published in article "Detecting very low allele fraction variants using targeted DNA sequencing and a novel molecular barcode-aware variant caller", BMC Genomics, 2017 18:5. https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-016-3425-4
smcounter-v2-paper
Data and code supporting smCounter-v2-paper