bcm-uga pcadapt issues - Githubissues

bcm-uga / pcadapt

Performing highly efficient genome scans for local adaptation with R package pcadapt v4

https://bcm-uga.github.io/pcadapt

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issues

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truncated p-values

#92 polobby closed 4 days ago
4
Can I use PCAadapt even if I don't have population structure?

#91 marce-herrera closed 3 weeks ago
15
Too many NA values

#90 Lin012345 closed 3 weeks ago
9
How to obtain the specific sites of outliers

#89 xiangping2023 opened 1 month ago
4
Eigenvalues and pcadapt for pooledSeq

#88 mroesti closed 2 months ago
2
Low explained Variance after LD clumping

#87 mehakmadhura closed 2 months ago
18
Help for using pcadapt with poolseq data

#86 ElMujtarVeronica closed 5 months ago
5
can not change Manhattan plot color

#85 WWz33 closed 3 months ago
3
PCADAPT error when higher K - can't compute SVD

#84 GabryS3 closed 6 months ago
6
MAF filters and p-value distribution.

#83 akamolphat opened 9 months ago
8
Error: Can't compute SVD.

#82 jcaccavo closed 10 months ago
0
Too many outliers

#81 sandyplus opened 1 year ago
13
Identifying snp positions of putatitively selected loci

#80 jayyeam closed 1 year ago
6
Allele frequency data can use in pcadapt?

#79 HengLiang1993 closed 10 months ago
5
pcadapt: variant(s) have been discarded as they are not SNPs

#78 KatherinOtalora closed 1 year ago
5
probelm with missing values

#77 cyadrogarcia closed 1 year ago
6
System is computationally singular error when using pcadapt on imported .bed file of simulated data

#76 jpfontenelle closed 2 years ago
5
How to extract genetic matrix from pcadapt object Inbox

#75 jpfontenelle closed 2 years ago
2
understanding pcadapt

#74 peter-civan closed 2 years ago
5
SNP significance plot looks strange

#73 NickJeff13 closed 2 years ago
1
ERROR reading .bed file - can't compute SDV

#72 VanELuz closed 2 years ago
0
Alternative to scree plot and score plot for K selection?

#71 jpfontenelle closed 2 years ago
2
Pooled samples?

#70 Tigeeeeer closed 2 years ago
1
Different sample size per population

#69 naborlozada closed 2 years ago
4
outlier SNP IDs from output

#68 Sistrurus-Steve closed 2 years ago
4
SNPs thinning LD clumping

#67 msalamon2 closed 2 years ago
1
How to get the genotype file

#66 hjt1129 closed 2 years ago
18
"missing values only" warning with data filtered to <0.1 missing values

#65 ewmorr closed 3 years ago
6
Is the new version of PCAdapt applicable to reduced representation population genomic datasets with 1000's of markers?

#64 ptcooper closed 3 years ago
1
Questions about K values

#63 weiwFu closed 3 years ago
8
Merge SNP position, maf and P-values.

#62 Ray569743422 closed 3 years ago
5
Modify figures

#61 kuratanp closed 3 years ago
3
Histogram of the P values

#60 domag closed 3 years ago
6
Loadings

#59 mbrieuc closed 3 years ago
12
Update plotUtils.R

#58 jbruxaux closed 3 years ago
1
Data filtering before analysis

#57 aydaraliev closed 3 years ago
12
Adding fake variants when you have too few.

#56 privefl closed 3 years ago
0
selecting K's and filtering criteria to use

#55 BelenJM closed 3 years ago
8
Importing loci ID

#54 marcticruz closed 3 years ago
12
Remove Outliers from data

#53 kwojtusik closed 3 years ago
1
How to obtain details of PCA drown by pcadapt

#52 Mary-00 closed 3 years ago
10
having memory issue when running PcAdapt with big data set

#51 shaghayeghsoudi closed 4 years ago
12
Feature request: Polyploid data

#50 ahmaduaf closed 3 years ago
3
LD clumping on Pool-Seq data

#49 apfuentes closed 4 years ago
15
ERROR: Can't compute SVD

#48 jrglass6 closed 4 years ago
18
Great difference of outliers detection using same cutoffs pcadapt/OutFlanks

#47 MaraRMinano closed 3 years ago
3
Singular values & proportion of explained variance

#46 YannDussert closed 4 years ago
14
variant(s) have been discarded as they are not SNPs

#45 tjmcgreevy closed 4 years ago
2
pcadapt() grabbing too many cores

#44 standard-aaron closed 4 years ago
5
Unexpected imputation in pcadapt.pcadapt_pool

#43 brandonlind closed 3 years ago
3