Sina Majidian's Projects
A pipline for haplotyping of 10x genomics
Copies of notebooks used in the practical sessions for Algorithms for DNA Sequencing
Slides for Algorithms for DNA Sequencing Coursera class
180+ Algorithm & Data Structure Problems using C++
A curated list of awesome Bioinformatics libraries and software.
:microscope: Path to a free self-taught education in Bioinformatics!
Conifer: Clonal Tree Inference for Tumor Heterogeneity with Single-Cell and Bulk Sequencing Data
Source Code and Starter Code for Accelerated Computer Science Fundamentals Specialization on Coursera
Convert input bam and vcf files to a fragment matrix
Infer exon level CNV from visium spatial data
Fragment matrix file: A format for extracting haplotype information from BAM and VCF file for polyploids (under test)
https://oma-stage.vital-it.ch/oma/academy/module/fastOMA_2023
FastOMA is a fast pipeline for species tree inference using placement in Hierarchical Orthologous Groups (HOGs).
repository of the 3-day course "First steps with Python in Life Sciences" from SIB-training
Python bindings to GenDisCal and addition of phylogenetic tree function
Precision pangenomics (review article on graph genomics)
Here are a set of example Relevant Background and Future Goals and Graduate Research Plan Statement statements for the NSF GRFP in Ecology and Evolutionary Biology.
A tool for reconstructing haplotypes polyploid genome using linked reads (10X Genomics).
software tools for haplotype assembly from sequence data
NGS based haplotype assembly using matrix completion
10x Genomics Reads Simulator
Evaluating MEC