A general 16S rDNA sequencing analysis pipeline

A workflow automation script: demultiplex the library sequence, run quality checks, deliver to archiving and processing afterwards

Lightweight library for parsing quality control information for the UMIs in 10x single cell gene expression assays

Lightweight standalone tool to reduce size of VCF files through filtering

Python code to detect ECGR Mutations; Takes a reference genome and bunch of reads as input and finds mutations (1-3 bp length) where number of supporting reads greater than 5

Trigenic interaction predictor in Python, using Mixed-Membership Stochastic Block Models

CoNSEnsX - Complience of NMR-derived Structural Ensembles with Experimental Data

A collection of Python modules equivalent to R ReQTL Toolkit aims to identify the association between expressed SNVs with their gene expression using RNA-sequencing data.

Pangenome-Analysis.py is written for extraction of core, accessory and unique genomes (Gene families and proteins) along with filtration of single copy orthologues, creation of binary and count matrices as well as removal of duplicates.

This is a collection of scripts for the bioinformatic analysis in the bachelor's thesis "Exploring the Potential of Camelid Single-Domain Antibodies: Structure, Properties and Diverse Applications in Therapeutics and Diagnostics" (2023). The scripts have been developed by Nora El-Zein, Nora Hemmingsson and Sara Mosebach.

Biological Data Analysis Library

2D Gini Index Implementation

Some solved problems of ROSALIND

A project on the evolution of genes of the crAssphage virus.

Predict Protein Stability Index from the sequence

RNA-Seq pipeline

BAMdelbee is a novel tool for discovering homozygous deletions in Whole-exome-sequencing (WES) and whole-genome-sequencing (WGS) data. WES or WGS samples generated by the same method produce BAM files with similar alignment coverage across the genome. BAMdelbee locates homozygous deletions by pinpointing regions covered in all samples but the on…

Sliding sampling and biological sequences