Mangul-Lab-USC/metadata-completeness

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Mangul-Lab-USC/HLA_benchmark

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Mangul-Lab-USC/Mangul-Lab-USC.github.io

Website for Mangul Lab.

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Mangul-Lab-USC/reTCR

TCR repertoire analysis in R

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Mangul-Lab-USC/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.

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Mangul-Lab-USC/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.

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Mangul-Lab-USC/code-availability

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Mangul-Lab-USC/VISTA

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Mangul-Lab-USC/imrep Fork of mandricigor/imrep

ImReP is a computational method for rapid and accurate profiling of the adaptive immune repertoire from regular RNA-Seq data.

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Mangul-Lab-USC/CXPT_599

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Mangul-Lab-USC/BioLLMBench

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Mangul-Lab-USC/CXPT-501-Fall_23

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Mangul-Lab-USC/ISBRA23 Fork of Mangul-Lab-USC/EBCG

https://mangul-lab-usc.github.io/ISBRA23/

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Mangul-Lab-USC/biomedical_data_science

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Mangul-Lab-USC/VISTA_paper

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Mangul-Lab-USC/COVID_bioinformatics

Code and figures for our COVID paper

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Mangul-Lab-USC/covid-genomics

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Mangul-Lab-USC/CXPT-599

Material for the course CXPT 599

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Mangul-Lab-USC/benchmarking_SV

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

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Mangul-Lab-USC/code-availability-temp

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Mangul-Lab-USC/EEBG2023 Fork of Mangul-Lab-USC/EBCG

https://mangul-lab-usc.github.io/EEBG2023/

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Mangul-Lab-USC/TCR-profiling-benchmark

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Mangul-Lab-USC/ISBRA22

https://mangul-lab-usc.github.io/ISBRA22/

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Mangul-Lab-USC/_ISBRA22

Website for ISBRA '22 conference

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Mangul-Lab-USC/pyTCR

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Mangul-Lab-USC/pyTCR_publication

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Mangul-Lab-USC/EM-GEDIT

GEDIT coupled with EM algorithm

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Mangul-Lab-USC/Bioinformatics-for-Ukraine

https://mangul-lab-usc.github.io/Bioinformatics-for-Ukraine/

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Mangul-Lab-USC/sbt

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Mangul-Lab-USC/metadata_sepsis

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Mangul-Lab-USC/EBCG

https://mangul-lab-usc.github.io/EBCG/

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Mangul-Lab-USC/enhancing_reproducibility

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Mangul-Lab-USC/benchmarking_error_correction

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

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Mangul-Lab-USC/Sepsis_prediction

The project tries to predict sepsis mortality from the cell type proportions.

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Mangul-Lab-USC/thesis-repository-template

This GitHub repository serves as an example of an organized file structure in which all steps of an analysis can be transparently presented.

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Mangul-Lab-USC/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.

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Mangul-Lab-USC/RNA-seq

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Mangul-Lab-USC/msc-thesis-Ruiwei-Guo

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Mangul-Lab-USC/db.microbiome

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Mangul-Lab-USC/benchmarking-transcriptomics-deconvolution

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

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Mangul-Lab-USC/Twitter-editorial

Repository has code, figures and paper for twitter editorial.

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Mangul-Lab-USC/TAIR

The Atlas of Immunoglobulin Repertoires (TheAIR)

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Mangul-Lab-USC/CXPT599_LAB_5 Fork of ramayyala/CXPT599_LAB_5

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Mangul-Lab-USC/Diversity-TCR-Seq

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Mangul-Lab-USC/ImReP_publication

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Mangul-Lab-USC/genomic-deserts

genomic-deserts

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Mangul-Lab-USC/genomics.USC.HPC

rna.seq.pipeline for USC HPC

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Mangul-Lab-USC/ImReP_publication_old

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Mangul-Lab-USC/sbt-publication

SBT_publication

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Mangul-Lab-USC/COVID-19-outbreak-investigations

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Mangul-Lab-USC/TCR-Seq-benchmarking

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

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Mangul-Lab-USC/cec

Computational education consortium

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Mangul-Lab-USC/sepsis

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Mangul-Lab-USC/immune-repertoires-vertebrate-species

Developing efficient and scalable bioinformatics methods and databases to analyze the adaptive immune repertoires across vertebrate species

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Mangul-Lab-USC/annie_project

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

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Mangul-Lab-USC/sanderslab.github.io Fork of sanderslab/sanderslab.github.io

The official website for Mangul Lan at USC

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Mangul-Lab-USC/pkg-manager-review

Manubot Repo for Package Manager Review Paper

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Mangul-Lab-USC/septic.shock.data

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Mangul-Lab-USC/Biomedical_workshop_assignment_part2_datasets

Download the data contained within the directory labeled by your email. Use this data to complete part2. There should be two files: 1) gene_matrix.csv and 2) meta_data.csv

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Mangul-Lab-USC/BMDW-Assignment-example

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Mangul-Lab-USC/Biomedical_workshop_assignment_part1_datasets

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Mangul-Lab-USC/RNA-SEQ-Tutorial-PART1

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Mangul-Lab-USC/UNIX-AND-USC-HPC

Tutorial on unix and navigating the USC HPC Cluster

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Mangul-Lab-USC/sbt_old

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

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Mangul-Lab-USC/presentations

repository for various presentations by members of Mangul lab at USC

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Mangul-Lab-USC/needle

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

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Mangul-Lab-USC/GEDITv1.4

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Mangul-Lab-USC/pseudo_map

A pseudo DNA/RNA mapping tool that selects the optimal package based on the read length.

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Mangul-Lab-USC/consistency_read_aligners

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Mangul-Lab-USC/project_skeleton

This is a skeleton of how future projects in the lab should be organized on Github.

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Mangul-Lab-USC/SLRG Fork of smangul1/SLRG

systematic library of reference genomes

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Mangul-Lab-USC/djoin Fork of smangul1/djoin

DJoin

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Mangul-Lab-USC/sv_method

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Mangul-Lab-USC/Packaging_bioinformatics_software

Packaging_bioinformatics_software

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Mangul-Lab-USC/benchmarking.error.correction.cleaned

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Mangul-Lab-USC/BWA_Tutorial

A tutorial for generating sequence alignments using BWA

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Mangul-Lab-USC/telescope Fork of QCB-Collaboratory/telescope

Telescope server repository

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Mangul-Lab-USC/seqtk Fork of aaronkarlsberg/seqtk

Toolkit for processing sequences in FASTA/Q formats

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Mangul-Lab-USC/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.

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Mangul-Lab-USC/GEDITv1.6

NewerVersionOfGEDIT

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Mangul-Lab-USC/Jupyter_Notebook_Tutorial

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Mangul-Lab-USC/clinical_metagenomics

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Mangul-Lab-USC/online.bioinformatics Fork of smangul1/online.bioinformatics

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