fastlmm/FaST-LMM issues and pull requests

#49 - Kinship

Issue - State: closed - Opened by snowformatics 16 days ago - 9 comments

#48 - Error in plotp.py: 'Legend' object has no attribute 'legendHandles'

Issue - State: open - Opened by vb-iman 20 days ago - 1 comment

#47 - q-values in single_snp() output?

Issue - State: closed - Opened by Jorge-Hernansanz 27 days ago - 2 comments

#46 - how to calculate phenotypic variance explained

Issue - State: closed - Opened by carrot881216 about 1 month ago - 1 comment

#45 - Using FaST-LMM single_snp() in a cluster server

Issue - State: closed - Opened by Jorge-Hernansanz about 2 months ago - 5 comments

#44 - Calculate heritability

Issue - State: closed - Opened by snowformatics about 2 months ago - 2 comments

#43 - Filtering on allele frequency and outputting allele frequency in result

Issue - State: closed - Opened by vb-iman about 2 months ago - 3 comments

#42 - warpedlmm installation

Issue - State: closed - Opened by asifzubair 2 months ago - 2 comments

#41 - TypeError in flutil.manhattan_plot()

Issue - State: closed - Opened by vb-iman 2 months ago - 7 comments

#40 - AttributeError; scipy vs numpy in utils

Issue - State: closed - Opened by vb-iman 3 months ago - 6 comments

#39 - PValue Output Format

Issue - State: closed - Opened by snowformatics 3 months ago - 16 comments

#38 - Remove links to nbviewer.org (notebooks don't need it anymore)

Issue - State: closed - Opened by snowformatics 5 months ago - 13 comments

#37 - Unable to run with multiple phenotypic traits together

Issue - State: closed - Opened by jefflllyyy 5 months ago - 1 comment

#36 - [Feature Request] Allow string as chromosom names

Issue - State: closed - Opened by snowformatics 11 months ago - 4 comments

#35 - ValueError: No individual observed for the SNP

Issue - State: closed - Opened by snowformatics about 1 year ago - 4 comments

#34 - FloatingPointError: divide by zero encountered in true_divide

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

#33 - Replacement for fastlmm.util.stats.quadform?

Issue - State: closed - Opened by yyang-peko over 1 year ago - 1 comment

#32 - Support cbgen>=1.0.1

Pull Request - State: closed - Opened by ofrei over 1 year ago - 4 comments

#31 - Ill-formed BED file. BED file header is incorrect or length is wrong

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

#30 - Run without PLINK format

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

#29 - epistatis test error

Issue - State: closed - Opened by snowformatics over 2 years ago - 8 comments

#28 - Hapmap format

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

#27 - Understanding SNPWeight Column and Conversion to Effect Size Estimation

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

#26 - When number of multiple phenotypes is large, run them in batches.

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

#25 - Scaling of beta estimates with case control analyses

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

#24 - How to tell which allele is used as reference for effect size estimates?

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

#23 - Some tests are skipped due to duplicate names fix

Pull Request - State: closed - Opened by code-review-doctor over 2 years ago - 1 comment

#22 - Some tests are skipped due to duplicate names

Issue - State: closed - Opened by code-review-doctor over 2 years ago - 1 comment

#21 - Scipy.dot and scipy.log etc are deprecated. Replace with numpy

Issue - State: closed - Opened by CarlKCarlK over 2 years ago

#20 - Issue with multiple phenotype files

Issue - State: closed - Opened by koa-planedin almost 3 years ago - 6 comments

#19 - Fatal Error : Expected a Chromosome in the form of an integer or a string X, Y, XY, or MT in file

Issue - State: closed - Opened by tinameiring about 3 years ago - 1 comment

#18 - Installing fast-lmm on CentOS 7

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

#17 - ValueError: No objects to concatenate

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

#16 - Epistatic interaction coefficient and error

Issue - State: closed - Opened by edinburgh-biomedical-ai about 3 years ago - 5 comments

#15 - Added color and ax options to manhattan_plot in util.py

Pull Request - State: open - Opened by lucasmiranda42 over 3 years ago

#14 - Result of single_snp analysis has fewer SNPs than input

Issue - State: closed - Opened by lucasmiranda42 over 3 years ago - 3 comments

#13 - fastlmm doesn't work with newest version of pip

Issue - State: closed - Opened by CarlKCarlK over 3 years ago

#12 - LMM.getPosteriorWeights() returns inconsitent results

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

#11 - GenDist is NaN after running single_snp analysis

Issue - State: closed - Opened by lucasmiranda42 over 3 years ago - 4 comments

#10 - Why did Bed.pos switch from int to float?

Issue - State: closed - Opened by remomomo over 3 years ago - 1 comment

#9 - SNPs from different replicons should be in one input file or separate?

Issue - State: closed - Opened by limin321 over 3 years ago - 3 comments

#8 - Installation problems on Windwos10

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

#7 - Adding ubuntu docker build + instructions

Pull Request - State: open - Opened by eric-czech about 4 years ago

GitHub / fastlmm/FaST-LMM issues and pull requests