AntonJMLarsson

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

stitcher.py

stitcher.py reconstructs molecules from Smart-seq3 data.

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).

NASC-seq

Code and analysis pipeline for NASC-seq.

NASC-seq2

Spreading-Correction

Supplementary information to "Computational correction of index switching in multiplexed sequencing libraries" (Larsson et. al 2018).

txburst

Transcriptional burst kinetics inference and analysis described in the article "Genomic encoding of transcriptional burst kinetics" (Larsson et. al 2019).

AntonJMLarsson/stitcher.py

stitcher.py reconstructs molecules from Smart-seq3 data.

AntonJMLarsson/antonjmlarsson.github.io

AntonJMLarsson/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).

AntonJMLarsson/clonal_mutations

AntonJMLarsson/counter-rs

Simple object to count Rust iterables

AntonJMLarsson/deepvariant

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

AntonJMLarsson/deML

Maximum likelihood demultiplexing

AntonJMLarsson/fastq-rs

AntonJMLarsson/flate2-rs

DEFLATE, gzip, and zlib bindings for Rust

AntonJMLarsson/lustre_snakemake_pipeline

A snakemake workflow for analyzing LUSTRE data.

AntonJMLarsson/mgatk

mgatk: mitochondrial genome analysis toolkit

AntonJMLarsson/Monopogen

SNV calling from single cell sequencing

AntonJMLarsson/MQuad

Tool for modelling of mitochondrial heteroplasmy

AntonJMLarsson/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

AntonJMLarsson/py-soft-impute

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

AntonJMLarsson/Scribe-py

Regulatory networks with Direct Information in python

AntonJMLarsson/scvi-tools

Deep probabilistic analysis of single-cell and spatial omics data

AntonJMLarsson/split_barcoded_bam

AntonJMLarsson/TALON

Technology agnostic long read analysis pipeline for transcriptomes

AntonJMLarsson/tama

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

AntonJMLarsson/vireo

Demultiplexing pooled scRNA-seq data with or without genotype reference