areebapatel Goto Github PK

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.

qiaseq-smcounter-v2

rapid-cns2

Rapid comprehensive adaptive nanopore-sequencing of CNS tumours set-up and analysis pipeline

rapid-cns2_nf

Rapid-CNS v2

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