• Stars
    star
    1
  • Language
    Jupyter Notebook
  • Created almost 5 years ago
  • Updated almost 5 years ago

Reviews

There are no reviews yet. Be the first to send feedback to the community and the maintainers!

Repository Details

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

More Repositories

1

benchmarking_SV

Updated figures for "A benchmarking of WGS-based structural variant callers" paper
Jupyter Notebook
24
star
2

benchmarking_error_correction

This is the GitHub repository for our benchmarking study "Benchmarking of computational error-correction methods for next-generation sequencing".
Jupyter Notebook
13
star
3

pyTCR

Jupyter Notebook
11
star
4

db.microbiome

Jupyter Notebook
7
star
5

Mangul-Lab-USC.github.io

Website for Mangul Lab.
Jupyter Notebook
7
star
6

TAIR

The Atlas of Immunoglobulin Repertoires (TheAIR)
Jupyter Notebook
7
star
7

RNA-seq

Jupyter Notebook
6
star
8

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
6
star
9

metadata_sepsis

Jupyter Notebook
5
star
10

enhancing_reproducibility

HTML
5
star
11

ImReP_publication_old

Jupyter Notebook
4
star
12

benchmarking-transcriptomics-deconvolution

Paper can be found here : https://academic.oup.com/bib/advance-article-abstract/doi/10.1093/bib/bbab265/6338547
C++
4
star
13

needle

Needle (full name: Needle in a haystack) combines alignment and assembly for comprehensive virome, mycobiome, and eukaryome profiling on the strain level.
Shell
4
star
14

biomedical_data_science

3
star
15

TCR-Seq-benchmarking

Comparison of Captured immune repertoire by TCR seq versus imrep, MIXCR, and TRUST4
Jupyter Notebook
3
star
16

TCR-profiling-benchmark

Jupyter Notebook
3
star
17

genomics.USC.HPC

rna.seq.pipeline for USC HPC
Shell
3
star
18

omics-data-reusability

Jupyter Notebook
2
star
19

septic.shock.data

Jupyter Notebook
2
star
20

ImReP_publication

Jupyter Notebook
2
star
21

pyTCR_publication

Jupyter Notebook
2
star
22

BioLLMBench

Jupyter Notebook
2
star
23

VISTA

Python
2
star
24

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
2
star
25

consistency_read_aligners

Python
1
star
26

COVID_bioinformatics

Code and figures for our COVID paper
Jupyter Notebook
1
star
27

Twitter-editorial

Repository has code, figures and paper for twitter editorial.
Jupyter Notebook
1
star
28

sbt

Shell
1
star
29

BWA_Tutorial

A tutorial for generating sequence alignments using BWA
C
1
star
30

pkg-manager-review

Manubot Repo for Package Manager Review Paper
HTML
1
star
31

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
1
star
32

sbt_old

Seeing Beyond the Target (SBT) - computational protocol to process off target reads in WXS experiments
Shell
1
star
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.
Jupyter Notebook
1
star