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antonjmlarsson.github.io

arme_and_bursting

Code for analysis described in the article "Transcriptional bursts explain autosomal random monoallelic expression and affect allelic imbalance" (Larsson et. al 2021).

clonal_mutations

counter-rs

Simple object to count Rust iterables

deepvariant

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

deml

Maximum likelihood demultiplexing

fastq-rs

flate2-rs

DEFLATE, gzip, and zlib bindings for Rust

mgatk

mgatk: mitochondrial genome analysis toolkit

monopogen

SNV calling from single cell sequencing

mquad

Tool for modelling of mitochondrial heteroplasmy

nasc-seq

Code and analysis pipeline for NASC-seq from NASC-seq monitors RNA synthesis in single cells Gerardus Hendriks, Lisa A Jung, Anton JM Larsson, Oscar Andersson Forsman, Michael Lidschreiber, Katja Lidschreiber, Patrick Cramer and Rickard Sandberg doi: https://doi.org/10.1101/498667

py-soft-impute

Python implementation of Mazumder and Hastie's softImpute for matrix completion

scribe-py

Regulatory networks with Direct Information in python

stitcher.py

stitcher.py reconstructs molecules from Smart-seq3 data.

talon

Technology agnostic long read analysis pipeline for transcriptomes

tama

Transcriptome Annotation by Modular Algorithms (for long read RNA sequencing data)

vireo

Demultiplexing pooled scRNA-seq data with or without genotype reference