mqondisi Goto Github PK

acpcoa

Adjustment for Confounding Factors using Principal Coordinate Analysis

alphabetr

R package for obtaining TCR alpha-beta sequence pairs

bam-readcount

count DNA sequence reads in BAM files

codex2

Full-spectrum copy number variation detection by high-throughput DNA sequencing

coding_exercise_tcga_infiltration

coding exercise using TCGA immune infiltration data

counting_sequences

Counting Sequences assignment for BSP 2015 Python course

covid_vax_cd8

Data and scripts for study Minervina, Pogorelyy et al. 2021

cutadapt

Cutadapt removes adapter sequences from sequencing reads

dandelion

dandelion - A single cell BCR-seq analysis package for 10X Chromium 5' data

deepvariant

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

findantibodies

A custom Python program to accompany Meyer et al. "A Simplified Workflow for Monoclonal Antibody Sequencing."

free_r_tips

Free R-Tips is a FREE Newsletter provided by Business Science. It comes with bite-sized code tutorials every week.

friendsdontletfriends

Friends don't let friends make certain types of data visualization - What are they and why are they bad.

gficf

An R implementation of the Gene Frequency - Inverse Cell Frequency method for single cell data normalization

igpipeline

imgthla

Github for files currently published in the IMGT/HLA FTP Directory hosted at the European Bioinformatics Institute

immunarch

🧬 Immunarch: an R Package for Fast and Painless Exploration of Single-cell and Bulk T-cell/Antibody Immune Repertoires

kbet

An R package to test for batch effects in high-dimensional single-cell RNA sequencing data.

kir_project

This is a repository to reproduce our KIR genotyping method (Sakaue et al.)

kpi

Structural interpretation of Killer cell immunoglobulin-like Receptors (KIR) haplotypes from raw short or long read sequences. It predicts the presence/absence of 16 KIR genes and then uses that to predict pairs of structural (gene-content and order) haplotypes.

matilda

Matilda is a multi-task framework for learning from single-cell multimodal omics data. Matilda leverages the information from the multi-modality of such data and trains a neural network model to simultaneously learn multiple tasks including data simulation, dimension reduction, visualization, classification, and feature selection.

mhc-prg

Population Reference Graphs for the HLA and MHC.

migmap

HTS-compatible wrapper for IgBlast V-(D)-J mapping tool

mixcr

MiXCR is an ultimate software platform for analysis of Next-Generation Sequencing (NGS) data for immune profiling.

mqondisi

Config files for my GitHub profile.

ngenomesyn

Any Way to Show Multi genomic Synteny

online_r_learning

Online R learning for applied statistics

phyloscanner

Phylogenetics between and within hosts at once, all along the genome.

prox-seq

Prox-seq is a single-cell sequencing assay developed by Tay Lab at the University of Chicago. Prox-seq can be used to obtain gene expression profile, and protein complex information in single cells. This is achieved by leveraging proximity ligation assay (PLA) with single-cell RNA-sequencing techniques.

pypop

Python for Population Genomics