sinamajidian
Bioinformatician | Postdoctoral Fellow at the Johns Hopkins University | Formerly at University of Lausanne & Wageningen University & Research.
Johns Hopkins UniversityBaltimore
Pinned Repositories
FastOMA
FastOMA is a scalable software package to infer orthology relationship.
omamo
OMAMO: orthology-based model organism selection
read2tree
a tool for inferring species tree from sequencing reads
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)
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).
phaseme
A tool set to assess the quality of the per read phasing and reduce the errors.
workshops
This repo contains the workshops that I have taught.
sinamajidian's Repositories
sinamajidian/EvANI
EvANI: genomic distance evaluation pipeline and benchmarking dataset
sinamajidian/extract_poly
Fragment matrix file: A format for extracting haplotype information from BAM and VCF file for polyploids (under test)
sinamajidian/fastoma_tree
FastOMA is a fast pipeline for species tree inference using placement in Hierarchical Orthologous Groups (HOGs).
sinamajidian/Hap10
A tool for reconstructing haplotypes polyploid genome using linked reads (10X Genomics).
sinamajidian/CNVanalysis
sinamajidian/workshops
This repo contains the workshops that I have taught.
sinamajidian/algorithms_and_data_structures
180+ Algorithm & Data Structure Problems using C++
sinamajidian/Awesome-Bioinformatics
A curated list of awesome Bioinformatics libraries and software.
sinamajidian/bioinformatics
:microscope: Path to a free self-taught education in Bioinformatics!
sinamajidian/Conifer
Conifer: Clonal Tree Inference for Tumor Heterogeneity with Single-Cell and Bulk Sequencing Data
sinamajidian/coursera_cpp
Source Code and Starter Code for Accelerated Computer Science Fundamentals Specialization on Coursera
sinamajidian/diploid_stratificiations
sinamajidian/exonCNV
Infer exon level CNV from visium spatial data
sinamajidian/FastOMA-academy
https://oma-stage.vital-it.ch/oma/academy/module/fastOMA_2023
sinamajidian/fastoma_repo_rooting
sinamajidian/first-steps-with-python-training
repository of the 3-day course "First steps with Python in Life Sciences" from SIB-training
sinamajidian/gendiscalpy
Python bindings to GenDisCal and addition of phylogenetic tree function
sinamajidian/mfb
sinamajidian/omamo
OMAMO: orthology-based model organism selection
sinamajidian/PhaseYou
sinamajidian/PoMoCNV
sinamajidian/read2tree
sinamajidian/read2tree-
a tool for inferring species tree from sequencing reads
sinamajidian/recombination
sinamajidian/SARS-CoV-2_workshop
sinamajidian/seq_learn_tutorial
:symbols: Code for the Sequence Learning Tutorial at BC2 2021 :nut_and_bolt:
sinamajidian/sinamajidian.github.io
Github Pages template for academic personal websites, forked from mmistakes/minimal-mistakes
sinamajidian/SURVIVOR
Toolset for SV simulation, comparison and filtering
sinamajidian/swat23-data-in-use
Tutorial for our submission to SWAT4HCLS "data-in-use"
sinamajidian/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.