caleblareau/Rpkgs caleblareau/Rpkgs

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caleblareau/Rpkgs
github

caleblareau

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Repository Details

A short presentation on R package logistics, creation, etc.

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

pearson_syndrome

Repository for reproducing analyses from Lareau et al. Nature Genetics 2023
R
5
star
14

indRop

An R package for basic indrop analyses and data handling
R
5
star
15

scLDSC

LD Score Regression in Single Cells
R
3
star
16

barcode-multiplets

Code and processed data to reproduce the barcode multiplet 10x paper
R
3
star
17

7076

Analysis of mtDNA variants that are synonymous, specifically m7076A>G
HTML
3
star
18

easyLift

R package for easy mm9 <-> mm10 / hg19 <-> hg38
R
3
star
19

shinyTeach

Short overview of basic shiny utility for purposes of teaching
R
3
star
20

asap_to_kite

CL python script to reformat CITEATAC fastqs for kite (kallisto | bustools) processing
Python
3
star
21

yolo

R package for handling large, sparse genomic data
R
2
star
22

split_bam_singlecell

Python functionality for splitting bam based on sam tag and dictionary
Python
2
star
23

k562-hichip

Simple workflow for analyzing multiple HiChIP replicate data with `diffloop`
R
2
star
24

chromVARxx

Additional functions added to chromVAR
R
1
star
25

pan-viral-reactivation

analyses of viral reactivation using single-cell sequencing
R
1
star
26

hisnpper

Toolkit for annotating bam files with haplotype SNVs
Python
1
star
27

document-mtdna-del

a
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