Ecosyste.ms: Issues

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GitHub / meyer-lab-cshl/plinkQC issues and pull requests

#54 - Issue with data pruning for ancestry estimation

Issue - State: open - Opened by safamajeed 8 months ago

#52 - Negative chromosome X heterozygosities

Issue - State: open - Opened by fastforward35 11 months ago - 1 comment

#51 - Negative Chr X heterozygosities

Issue - State: open - Opened by fastforward35 11 months ago

#50 - Updates for Ancestry Estimation Vignette

Issue - State: open - Opened by carolinewalter5 almost 2 years ago

#49 - 1000 Genomes phase 3 links have changed

Issue - State: open - Opened by mxhm over 2 years ago

#48 - Error using the evaluate_check_ancestry function

Issue - State: open - Opened by boseb over 2 years ago - 1 comment

#47 - Some questions about ancestry estimation

Issue - State: open - Opened by jordur over 2 years ago

#46 - Cannot find sample in the prefix merged dataset

Issue - State: closed - Opened by rskl92 over 2 years ago - 1 comment

#45 - mkdir flag

Pull Request - State: closed - Opened by eg-r almost 3 years ago

#44 - Dev

Pull Request - State: closed - Opened by HannahVMeyer about 3 years ago

#43 - check_snp_missingness error

Issue - State: closed - Opened by nickorr78 over 3 years ago - 3 comments

#42 - check_relatedness ignores genomebuild

Issue - State: closed - Opened by fechva over 3 years ago - 2 comments

#41 - plinkQC a single sample

Issue - State: closed - Opened by jielab over 3 years ago - 3 comments

#40 - Update dplyr verb syntax avoiding global variable issues

Pull Request - State: closed - Opened by HannahVMeyer over 3 years ago

#39 - Update github to 0.3.3

Pull Request - State: closed - Opened by HannahVMeyer over 3 years ago

#38 - Ancestry Check outlier mapping

Issue - State: closed - Opened by pwuUCL over 3 years ago - 5 comments
Labels: enhancement

#37 - Error in evaluate_ancestry_check samples that cannot be found

Issue - State: closed - Opened by brkicd over 3 years ago - 6 comments

#36 - Zooming in on PCA graph?

Issue - State: closed - Opened by MichaelCummingsBCH almost 4 years ago

#35 - plot was not created

Issue - State: closed - Opened by montenegrina almost 4 years ago - 2 comments

#34 - Build version

Issue - State: closed - Opened by montenegrina about 4 years ago - 2 comments

#33 - markerQC

Issue - State: closed - Opened by umasaxena about 4 years ago - 2 comments

#32 - Dev

Pull Request - State: closed - Opened by HannahVMeyer about 4 years ago

#31 - name.fail-IBD.IDs not found

Issue - State: closed - Opened by wiedenhoeft about 4 years ago - 6 comments

#30 - check_sex fails if no gender mismatch is found in the data

Issue - State: closed - Opened by pasiunaite about 4 years ago - 2 comments

#29 - Dev

Pull Request - State: closed - Opened by HannahVMeyer about 4 years ago

#28 - Unknown error using the evaluate_check_ancestry function

Issue - State: closed - Opened by MichaelCummingsBCH over 4 years ago - 33 comments

#27 - X chromosome QC

Issue - State: closed - Opened by rskl92 over 4 years ago - 10 comments
Labels: question

#26 - ERROR WHILE RUNNING PLINKQC IN RSTUDIO ON WINDOWS

Issue - State: closed - Opened by hkiran22 over 4 years ago - 4 comments

#25 - Shifted PCA plots with respect to reference sample

Issue - State: closed - Opened by HannahVMeyer over 4 years ago - 37 comments

#24 - A<->T and C<->G lead to shift population shifts in ancestry qc

Issue - State: closed - Opened by HannahVMeyer over 4 years ago - 2 comments

#23 - Relatedness checks

Issue - State: closed - Opened by rskl92 over 4 years ago - 15 comments

#22 - Dev

Pull Request - State: closed - Opened by HannahVMeyer over 4 years ago - 1 comment

#21 - Log issue occurs when running the function perMarkerQC and overviewPerMarkerQC

Issue - State: closed - Opened by fanwayne over 4 years ago - 5 comments
Labels: enhancement, help wanted

#20 - Alleles swapped in cleanData

Issue - State: closed - Opened by evagradovich almost 5 years ago - 2 comments

#19 - Dev

Pull Request - State: closed - Opened by HannahVMeyer almost 5 years ago

#18 - Dev

Pull Request - State: closed - Opened by HannahVMeyer about 5 years ago

#17 - Dev

Pull Request - State: closed - Opened by HannahVMeyer about 5 years ago

#16 - Error when running overviewPerIndividualQC function

Issue - State: closed - Opened by dietmarfdz about 5 years ago - 4 comments

#15 - Exit error in relatedness check

Issue - State: closed - Opened by evagradovich about 5 years ago - 2 comments

#14 - evaluate_check_ancestry fails with numeric IDs

Issue - State: closed - Opened by Rodin67 about 5 years ago - 2 comments

#13 - Dev

Pull Request - State: closed - Opened by HannahVMeyer about 5 years ago

#12 - Dev

Pull Request - State: closed - Opened by HannahVMeyer about 5 years ago

#11 - Possible Bug relatednessFilter

Issue - State: closed - Opened by GabrieleNocchi about 5 years ago - 24 comments

#10 - Error when following Genomes1000.Rmd commands

Issue - State: closed - Opened by dpcc2 about 5 years ago - 2 comments
Labels: help wanted

#9 - macTh and mafTh in perMarkerQC

Issue - State: closed - Opened by blueskypie about 5 years ago - 3 comments
Labels: invalid

#8 - error from perMarkerQC

Issue - State: closed - Opened by blueskypie about 5 years ago - 4 comments

#7 - error from overviewPerIndividualQC

Issue - State: closed - Opened by blueskypie about 5 years ago - 1 comment

#6 - error from overviewPerIndividualQC

Issue - State: closed - Opened by blueskypie over 5 years ago - 2 comments
Labels: bug

#5 - perIndividualQC

Issue - State: closed - Opened by blueskypie over 5 years ago - 1 comment
Labels: enhancement

#3 - error running relateness check

Issue - State: closed - Opened by blueskypie over 5 years ago - 11 comments

#2 - Removing failed IDs

Issue - State: closed - Opened by eg-r over 5 years ago - 1 comment

#1 - Wrong system call for windows

Issue - State: closed - Opened by HannahVMeyer almost 6 years ago - 1 comment
Labels: bug