Explore @Mangul-Lab-USC Open Source projects

@Mangul-Lab-USC

Mangul-Lab-USC

Stars
152
Global Org. Rank 46,827 (Top 15 %)
Registered about 5 years ago
Most used languages

Jupyter Notebook
69.7 %

Shell
12.1 %

HTML
6.1 %

Python
6.1 %

C
3.0 %

C++
3.0 %

benchmarking_SV

Updated figures for "A benchmarking of WGS-based structural variant callers" paper

Jupyter Notebook

benchmarking_error_correction

This is the GitHub repository for our benchmarking study "Benchmarking of computational error-correction methods for next-generation sequencing".

Jupyter Notebook

pyTCR

Jupyter Notebook

db.microbiome

Jupyter Notebook

Mangul-Lab-USC.github.io

Website for Mangul Lab.

Jupyter Notebook

TAIR

The Atlas of Immunoglobulin Repertoires (TheAIR)

Jupyter Notebook

RNA-seq

Jupyter Notebook

review-technology-dictates-algorithms

A systematic survey of algorithmic foundations and methodologies across 107 alignment methods (1988-2021), for both short and long reads. We provide a rigorous experimental evaluation of 11 read aligners to demonstrate the effect of these underlying algorithms on speed and efficiency of read alignment. Described by Alser et al. at https://arxiv.org/abs/2003.00110.

Jupyter Notebook

metadata_sepsis

Jupyter Notebook

enhancing_reproducibility

ImReP_publication_old

Jupyter Notebook

benchmarking-transcriptomics-deconvolution

Paper can be found here : https://academic.oup.com/bib/advance-article-abstract/doi/10.1093/bib/bbab265/6338547

needle

Needle (full name: Needle in a haystack) combines alignment and assembly for comprehensive virome, mycobiome, and eukaryome profiling on the strain level.

biomedical_data_science

TCR-Seq-benchmarking

Comparison of Captured immune repertoire by TCR seq versus imrep, MIXCR, and TRUST4

Jupyter Notebook

TCR-profiling-benchmark

Jupyter Notebook

genomics.USC.HPC

rna.seq.pipeline for USC HPC

omics-data-reusability

Jupyter Notebook

septic.shock.data

Jupyter Notebook

ImReP_publication

Jupyter Notebook

pyTCR_publication

Jupyter Notebook

BioLLMBench

Jupyter Notebook

VISTA

Introduction-to-bioinformatics-and-biomedical-data-science

This is a six module graduate-level course covering the fundamentals of transparent and reproducible bioinformatics, targeted towards biomedical students.

Jupyter Notebook

consistency_read_aligners

COVID_bioinformatics

Code and figures for our COVID paper

Jupyter Notebook

Twitter-editorial

Repository has code, figures and paper for twitter editorial.

Jupyter Notebook

sbt

BWA_Tutorial

A tutorial for generating sequence alignments using BWA

pkg-manager-review

Manubot Repo for Package Manager Review Paper

omics-packaging-containerizing

This is the GitHub repository for our recent study "Packaging and containerizing of bioinformatics software: advances, challenges, and opportunities" Please follow to the repository's wiki for more information and details on how this repository is connected to the paper.

Jupyter Notebook

annie_project

clonality and cell type composition of patients with persistent bacteremia. Extracted from bulk RNA Seq Data.

Jupyter Notebook

sbt_old

Seeing Beyond the Target (SBT) - computational protocol to process off target reads in WXS experiments

technology.dictates.algorithms

This is the GitHub repository for our recent study "Technology dictates algorithms : Recent developments in read alignments." Please follow to the repository's wiki for more information and details on how this repository is connected to the paper.

Jupyter Notebook