Skip to content

brianpenghe/linuxshell-genomics

BranchesTags

Folders and files

NameName
Last commit message
Last commit date

Latest commit

 

History

60 Commits
10X2snap.sh
10X2snap.sh
 
 
BaseMountLira.sh
BaseMountLira.sh
 
 
CellRangerATAC.sh
CellRangerATAC.sh
 
 
CellRangerRun.sh
CellRangerRun.sh
 
 
CellRangerVDJ.sh
CellRangerVDJ.sh
 
 
CellrangerATAC_at_farm.sh
CellrangerATAC_at_farm.sh
 
 
CellrangerSummary.sh
CellrangerSummary.sh
 
 
CellrangerVDJSummary.sh
CellrangerVDJSummary.sh
 
 
CheckFastqgzs.sh
CheckFastqgzs.sh
 
 
CheckFastqs.sh
CheckFastqs.sh
 
 
CompressVCF.sh
CompressVCF.sh
 
 
Extract3primeFromFastq.sh
Extract3primeFromFastq.sh
 
 
FlagBAM.py
FlagBAM.py
 
 
GetSeqAFromB.sh
GetSeqAFromB.sh
 
 
HCAupload-ATAC.sh
HCAupload-ATAC.sh
 
 
HCAupload.sh
HCAupload.sh
 
 
InstallBaseMount.sh
InstallBaseMount.sh
 
 
KrisStarsoloSummary.sh
KrisStarsoloSummary.sh
 
 
PlateTo10XFastq.sh
PlateTo10XFastq.sh
 
 
README.md
README.md
 
 
SubsetCellrangerBam.sh
SubsetCellrangerBam.sh
 
 
cramfastq.sh
cramfastq.sh
 
 
cramfastq10XATAC.sh
cramfastq10XATAC.sh
 
 
fix-souporcell-vcf-for-cellranger2020A.sh
fix-souporcell-vcf-for-cellranger2020A.sh
 
 
iRODS_download_path.sh
iRODS_download_path.sh
 
 
iRODSdownloader.sh
iRODSdownloader.sh
 
 
iRODSdownloaderBCR.sh
iRODSdownloaderBCR.sh
 
 
iRODSdownloaderTCR.sh
iRODSdownloaderTCR.sh
 
 
iRODSdownloader_10XATAC.sh
iRODSdownloader_10XATAC.sh
 
 
iRODSdownloader_10XATAC_CellRangerATAC.sh
iRODSdownloader_10XATAC_CellRangerATAC.sh
 
 
iRODSdownloader_10XATAC_CellRangerATAC_big2farm.sh
iRODSdownloader_10XATAC_CellRangerATAC_big2farm.sh
 
 
iRODSdownloader_CellRangerRunGEX.sh
iRODSdownloader_CellRangerRunGEX.sh
 
 
iRODSdownloader_CellRangerRunGEX5prime.sh
iRODSdownloader_CellRangerRunGEX5prime.sh
 
 
iRODSdownloader_CheckMeta.sh
iRODSdownloader_CheckMeta.sh
 
 
iRODSshowLane.sh
iRODSshowLane.sh
 
 
souporcell_all.sh
souporcell_all.sh
 
 

Repository files navigation

⚠️⚠️Repo MOVED to HERE ⚠️⚠️!

⚠️⚠️Updated Folder HERE ⚠️⚠️!

⚠️⚠️Newer version HERE ⚠️⚠️!

About

A set of basic scripts to handle genomics tasks using linux shell

Resources

Readme
Activity

Stars

1 star

Watchers

1 watching

Forks

1 fork
Report repository

Releases

No releases published

Packages

No packages published

Languages