sinamajidian

fastoma_tree

FastOMA is a fast pipeline for species tree inference using placement in Hierarchical Orthologous Groups (HOGs).

Hap10

A tool for reconstructing haplotypes polyploid genome using linked reads (10X Genomics).

CNVanalysis

EvANI

EvANI: genomic distance evaluation pipeline and benchmarking dataset

extract_poly

Fragment matrix file: A format for extracting haplotype information from BAM and VCF file for polyploids (under test)

workshops

This repo contains the workshops that I have taught.

algorithms_and_data_structures

180+ Algorithm & Data Structure Problems using C++

Awesome-Bioinformatics

A curated list of awesome Bioinformatics libraries and software.

bioinformatics

:microscope: Path to a free self-taught education in Bioinformatics!

Conifer

Conifer: Clonal Tree Inference for Tumor Heterogeneity with Single-Cell and Bulk Sequencing Data

coursera_cpp

Source Code and Starter Code for Accelerated Computer Science Fundamentals Specialization on Coursera

diploid_stratificiations

exonCNV

Infer exon level CNV from visium spatial data

FastOMA-academy

https://oma-stage.vital-it.ch/oma/academy/module/fastOMA_2023

fastoma_repo_rooting

first-steps-with-python-training

repository of the 3-day course "First steps with Python in Life Sciences" from SIB-training

gendiscalpy

Python bindings to GenDisCal and addition of phylogenetic tree function

mfb

omamo

OMAMO: orthology-based model organism selection

PhaseYou

PoMoCNV

read2tree

read2tree-

a tool for inferring species tree from sequencing reads

recombination

SARS-CoV-2_workshop

seq_learn_tutorial

:symbols: Code for the Sequence Learning Tutorial at BC2 2021 :nut_and_bolt:

sinamajidian.github.io

Github Pages template for academic personal websites, forked from mmistakes/minimal-mistakes

SURVIVOR

Toolset for SV simulation, comparison and filtering

swat23-data-in-use

Tutorial for our submission to SWAT4HCLS "data-in-use"

UNIL_MLS_Master_FS_HOG_WGD_Detection

Python code for quantitative and comparative analysis of hierarchical orthologous groups to place whole genome duplication events on a phylogenetic tree of a given set of organisms.