• Stars
    star
    5
  • Rank 2,847,522 (Top 57 %)
  • Language
    R
  • Created over 4 years ago
  • Updated about 1 year ago

Reviews

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

Repository Details

Repository for reproducing analyses from Lareau et al. Nature Genetics 2023

More Repositories

1

mgatk

mgatk: mitochondrial genome analysis toolkit
Python
100
star
2

BuenColors

R package of colors for the Buenrostro Lab
R
78
star
3

gchromVAR

Cell type specific enrichments using finemapped variants and quantitative epigenetic data
R
42
star
4

bap

Bead-based single-cell atac processing
Python
31
star
5

asap_reproducibility

Reproducing all analyses and figures for the ASAP-seq paper
Jupyter Notebook
29
star
6

singlecell_bloodtraits

Data/analysis repository for "Interrogation of human hematopoiesis..." paper
R
18
star
7

immune_cell_signature_genes

Repository for signature genes from Immune Cell Atlas
R
18
star
8

maegatk

Mitochondrial Alteration Enrichment and Genome Analysis Toolkit
Python
17
star
9

mitoblacklist

Repo for generating custom blacklist for reads originating from mitochondrial DNA to nuclear genome
Shell
16
star
10

mtscATACpaper_reproducibility

Repository to reproduce all analyses for Lareau*, Ludwig*, et al. 2020
HTML
15
star
11

proatac

Preprocessing pipeline for (sc)ATAC data
Python
10
star
12

mtscatac_protocol

Repository for mtscATAC-seq protocol paper
R
6
star
13

indRop

An R package for basic indrop analyses and data handling
R
5
star
14

scLDSC

LD Score Regression in Single Cells
R
3
star
15

barcode-multiplets

Code and processed data to reproduce the barcode multiplet 10x paper
R
3
star
16

7076

Analysis of mtDNA variants that are synonymous, specifically m7076A>G
HTML
3
star
17

easyLift

R package for easy mm9 <-> mm10 / hg19 <-> hg38
R
3
star
18

shinyTeach

Short overview of basic shiny utility for purposes of teaching
R
3
star
19

asap_to_kite

CL python script to reformat CITEATAC fastqs for kite (kallisto | bustools) processing
Python
3
star
20

yolo

R package for handling large, sparse genomic data
R
2
star
21

split_bam_singlecell

Python functionality for splitting bam based on sam tag and dictionary
Python
2
star
22

k562-hichip

Simple workflow for analyzing multiple HiChIP replicate data with `diffloop`
R
2
star
23

chromVARxx

Additional functions added to chromVAR
R
1
star
24

pan-viral-reactivation

analyses of viral reactivation using single-cell sequencing
R
1
star
25

hisnpper

Toolkit for annotating bam files with haplotype SNVs
Python
1
star
26

document-mtdna-del

a
1
star
27

Rpkgs

A short presentation on R package logistics, creation, etc.
HTML
1
star
28

mouse-brain-sequences

Repository to facilitate sequence generation from peaks
R
1
star
29

snp-query-sequences

R/Bioconductor workflow for grabbing sequences surrounding specified variants / genomic positions
R
1
star
30

cshl-ast2019-scATAC

Material for Advanced Sequencing Technologies pratical on scATAC-seq
HTML
1
star
31

redeem-reanalysis-reproducibility

CL repository for reproducing ReDeeM reanalyses
R
1
star