Rosemeis/pcangsd issues and pull requests

#87 - ZeroDivisionError: float division by zero, new "old" error

Issue - State: open - Opened by cbossu 8 months ago - 1 comment

#86 - pcangsd didn't converge!!

Issue - State: open - Opened by NeethuCherukuri 9 months ago - 6 comments

#86 - pcangsd didn't converge!!

Issue - State: open - Opened by NeethuCherukuri 9 months ago - 6 comments

#85 - zcat: can't stat

Issue - State: closed - Opened by EwersAquaGenomics 10 months ago - 1 comment

#85 - zcat: can't stat

Issue - State: closed - Opened by EwersAquaGenomics 10 months ago - 1 comment

#84 - -sites_save returning only 0s

Issue - State: closed - Opened by nickylustenhouwer 12 months ago - 3 comments

#84 - -sites_save returning only 0s

Issue - State: closed - Opened by nickylustenhouwer 12 months ago - 3 comments

#83 - Import Error

Issue - State: open - Opened by isnmn about 1 year ago - 6 comments

#83 - Import Error

Issue - State: open - Opened by isnmn about 1 year ago - 6 comments

#82 - How is the K chosen in the program?

Issue - State: open - Opened by yksakana about 1 year ago - 4 comments

#82 - How is the K chosen in the program?

Issue - State: open - Opened by yksakana about 1 year ago - 4 comments

#81 - -sites_save option outputs zero value for all markers

Issue - State: closed - Opened by yksakana about 1 year ago - 2 comments

#80 - build failure when installing with conda

Issue - State: open - Opened by nrcombs about 1 year ago - 1 comment

#79 - Packaging in Conda

Issue - State: open - Opened by lecorguille about 1 year ago - 1 comment

#79 - Packaging in Conda

Issue - State: open - Opened by lecorguille about 1 year ago - 1 comment

#78 - latest version (1.10) has not been tagged

Issue - State: closed - Opened by jowodo about 1 year ago - 3 comments

#77 - P-values equal to 0 from pcadapt

Issue - State: open - Opened by akimmitt about 1 year ago - 7 comments

#77 - P-values equal to 0 from pcadapt

Issue - State: open - Opened by akimmitt about 1 year ago - 7 comments

#76 - request: add SNP locus metadata to SNP weights output?

Issue - State: open - Opened by TeresaPegan over 1 year ago - 1 comment

#75 - Adding a pyproject.toml file

Issue - State: closed - Opened by alxsimon over 1 year ago - 3 comments

#75 - Adding a pyproject.toml file

Issue - State: closed - Opened by alxsimon over 1 year ago - 3 comments

#74 - Feature Request: Improved Convergence Checking

Issue - State: open - Opened by ajasonowicz over 1 year ago - 2 comments

#74 - Feature Request: Improved Convergence Checking

Issue - State: open - Opened by ajasonowicz over 1 year ago - 2 comments

#73 - SNP loading values from PCs using --selection_e

Issue - State: open - Opened by HomereAMK over 1 year ago - 3 comments

#72 - Kinship matrix in pcangsd

Issue - State: open - Opened by ThibauldMichel over 1 year ago - 1 comment

#72 - Kinship matrix in pcangsd

Issue - State: open - Opened by ThibauldMichel over 1 year ago - 1 comment

#71 - cannot import name 'reader_cy' from 'pcangsd'

Issue - State: open - Opened by cnxiaobo94 almost 2 years ago - 3 comments

#71 - cannot import name 'reader_cy' from 'pcangsd'

Issue - State: open - Opened by cnxiaobo94 almost 2 years ago - 3 comments

#70 - output of -selection

Issue - State: open - Opened by shirasegoby almost 2 years ago - 5 comments

#70 - output of -selection

Issue - State: open - Opened by shirasegoby almost 2 years ago - 5 comments

#69 - ImportError: cannot import name 'reader_cy' from pcangsd

Issue - State: closed - Opened by ashno376 almost 2 years ago - 1 comment

#69 - ImportError: cannot import name 'reader_cy' from pcangsd

Issue - State: closed - Opened by ashno376 almost 2 years ago - 1 comment

#68 - Different result among versions, same dataset

Issue - State: open - Opened by Ittybittyweeny almost 2 years ago - 4 comments

#68 - Different result among versions, same dataset

Issue - State: open - Opened by Ittybittyweeny almost 2 years ago - 4 comments

#67 - Confussion between tutorials

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

#67 - Confussion between tutorials

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

#66 - How to format a --filterSites file?

Issue - State: open - Opened by TeresaPegan almost 2 years ago - 1 comment

#66 - How to format a --filterSites file?

Issue - State: open - Opened by TeresaPegan almost 2 years ago - 1 comment

#65 - How to perform a HWE test?

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

#65 - How to perform a HWE test?

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

#64 - PCAngsd detects one fewer sites than it's given

Issue - State: open - Opened by jtoy7 about 2 years ago - 4 comments

#64 - PCAngsd detects one fewer sites than it's given

Issue - State: open - Opened by jtoy7 about 2 years ago - 4 comments

#63 - How to resolve an apparent memory issue PCAngsd

Issue - State: open - Opened by BKrek89 over 2 years ago - 3 comments

#63 - How to resolve an apparent memory issue PCAngsd

Issue - State: open - Opened by BKrek89 over 2 years ago - 3 comments

#62 - Cynthonization behaving strangely

Issue - State: open - Opened by ghost over 2 years ago - 6 comments

#62 - Cynthonization behaving strangely

Issue - State: open - Opened by ghost over 2 years ago - 6 comments

#61 - Cythonized pcangsd.py not working

Issue - State: closed - Opened by emrullahub over 2 years ago - 11 comments

#61 - Cythonized pcangsd.py not working

Issue - State: closed - Opened by emrullahub over 2 years ago - 11 comments

#60 - Segmentation fault (core dumped)

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

#60 - Segmentation fault (core dumped)

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

#59 - Support for VCF input

Issue - State: open - Opened by fgvieira almost 3 years ago

#58 - [Support] Using PCAngsdv2 to determine kinship

Issue - State: open - Opened by fidibidi almost 3 years ago

#58 - [Support] Using PCAngsdv2 to determine kinship

Issue - State: open - Opened by fidibidi almost 3 years ago

#57 - expected unicode, got str

Issue - State: closed - Opened by yungsiyebu about 3 years ago - 5 comments

#57 - expected unicode, got str

Issue - State: closed - Opened by yungsiyebu about 3 years ago - 5 comments

#56 - Selection scan - positions?

Issue - State: open - Opened by hyperoplus about 3 years ago - 5 comments

#56 - Selection scan - positions?

Issue - State: open - Opened by hyperoplus about 3 years ago - 5 comments

#55 - Negative eigenvalues

Issue - State: open - Opened by elizeng about 3 years ago - 1 comment

#55 - Negative eigenvalues

Issue - State: open - Opened by elizeng about 3 years ago - 1 comment

#54 - No module named 'reader_cy'

Issue - State: closed - Opened by DcornishUCL about 3 years ago - 7 comments

#54 - No module named 'reader_cy'

Issue - State: closed - Opened by DcornishUCL about 3 years ago - 7 comments

#53 - Sample projection

Issue - State: closed - Opened by xinsun1 over 3 years ago - 2 comments

#53 - Sample projection

Issue - State: closed - Opened by xinsun1 over 3 years ago - 2 comments

#52 - Reformating for easier packaging

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

#52 - Reformating for easier packaging

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

#51 - Genotype likelihood matrix format inside pcangsd (L)

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

#50 - Memory issue while parsing beagle file

Issue - State: closed - Opened by ddenney1 over 3 years ago - 2 comments

#50 - Memory issue while parsing beagle file

Issue - State: closed - Opened by ddenney1 over 3 years ago - 2 comments

#49 - Inflated p-values from selection scan?

Issue - State: open - Opened by kellybarr over 3 years ago - 8 comments

#48 - TypeError: 'offset' is an invalid keyword argument for fromfile()

Issue - State: open - Opened by samarth8392 over 3 years ago - 1 comment

#47 - NJ Tree and PCAdapt outputs

Issue - State: closed - Opened by emilya21 almost 4 years ago - 3 comments

#46 - error: "Argument 'beagle' has incorrect type"

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

#46 - error: "Argument 'beagle' has incorrect type"

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

#45 - UnboundLocalError: local variable 'pr' referenced before assignment

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

#45 - UnboundLocalError: local variable 'pr' referenced before assignment

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

#44 - -filter error

Issue - State: closed - Opened by alxsimon almost 4 years ago - 7 comments

#44 - -filter error

Issue - State: closed - Opened by alxsimon almost 4 years ago - 7 comments

#43 - PC loadings?

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

#43 - PC loadings?

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

#42 - Large log likelihood when running Admixture

Issue - State: open - Opened by bpbentley almost 4 years ago - 2 comments

#42 - Large log likelihood when running Admixture

Issue - State: open - Opened by bpbentley almost 4 years ago - 2 comments

#41 - PCA performance with low depth and low sample size

Issue - State: closed - Opened by nicolas931010 about 4 years ago - 6 comments

#41 - PCA performance with low depth and low sample size

Issue - State: closed - Opened by nicolas931010 about 4 years ago - 6 comments

#40 - Add a -sites flag

Issue - State: open - Opened by silastittes about 4 years ago

#40 - Add a -sites flag

Issue - State: open - Opened by silastittes about 4 years ago

#39 - Selection scan power?

Issue - State: open - Opened by mpinsky over 4 years ago - 8 comments

#39 - Selection scan power?

Issue - State: open - Opened by mpinsky over 4 years ago - 8 comments

#38 - Problem running pcangsd on mac because of zcat

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

#38 - Problem running pcangsd on mac because of zcat

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

#37 - stuck at "loading site information"

Issue - State: open - Opened by z0on over 4 years ago

#37 - stuck at "loading site information"

Issue - State: open - Opened by z0on over 4 years ago

#36 - gzip: stdout: Broken pipe

Issue - State: closed - Opened by DrLaurenCWhite over 4 years ago - 1 comment

#36 - gzip: stdout: Broken pipe

Issue - State: closed - Opened by DrLaurenCWhite over 4 years ago - 1 comment

#35 - How to get the proportion of variances explained by PCs?

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

#35 - How to get the proportion of variances explained by PCs?

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

#34 - PCAngsd -selection error

Issue - State: closed - Opened by jenncoughlan over 4 years ago - 3 comments

#34 - PCAngsd -selection error

Issue - State: closed - Opened by jenncoughlan over 4 years ago - 3 comments

#33 - pcangsd error

Issue - State: closed - Opened by biozzq over 4 years ago - 1 comment

#33 - pcangsd error

Issue - State: closed - Opened by biozzq over 4 years ago - 1 comment

#32 - cythonizing reader.pyx

Issue - State: open - Opened by ovidp over 4 years ago

GitHub / Rosemeis/pcangsd issues and pull requests