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Repository Details

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1

benchmarking_SV

Updated figures for "A benchmarking of WGS-based structural variant callers" paper
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2

benchmarking_error_correction

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3

pyTCR

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4

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Website for Mangul Lab.
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5

TAIR

The Atlas of Immunoglobulin Repertoires (TheAIR)
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6

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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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8

metadata_sepsis

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9

enhancing_reproducibility

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10

ImReP_publication_old

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11

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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12

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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13

biomedical_data_science

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14

TCR-Seq-benchmarking

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15

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16

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rna.seq.pipeline for USC HPC
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17

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18

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19

ImReP_publication

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20

pyTCR_publication

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21

BioLLMBench

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22

VISTA

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23

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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24

consistency_read_aligners

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25

COVID_bioinformatics

Code and figures for our COVID paper
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26

Twitter-editorial

Repository has code, figures and paper for twitter editorial.
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27

sbt

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28

BWA_Tutorial

A tutorial for generating sequence alignments using BWA
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29

pkg-manager-review

Manubot Repo for Package Manager Review Paper
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1
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30

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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31

annie_project

clonality and cell type composition of patients with persistent bacteremia. Extracted from bulk RNA Seq Data.
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32

sbt_old

Seeing Beyond the Target (SBT) - computational protocol to process off target reads in WXS experiments
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33

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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1
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