Ecosyste.ms: Issues

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GitHub / fastlmm/FaST-LMM issues and pull requests

#54 - update fastlmm package in bioconda channel

Issue - State: closed - Opened by JorgeHB14 2 months ago - 3 comments

#53 - ValueError: No individual observed for the SNP

Issue - State: closed - Opened by AbestSG 6 months ago - 2 comments

#52 - synthetic dataset documentation

Issue - State: open - Opened by snowformatics 6 months ago - 1 comment

#51 - single_snp with large number of SNPs

Issue - State: open - Opened by snowformatics 7 months ago - 5 comments

#50 - using only one chromosome

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

#49 - Kinship

Issue - State: closed - Opened by snowformatics 8 months ago - 9 comments

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

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

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

Issue - State: closed - Opened by Jorge-Hernansanz 8 months ago - 2 comments

#46 - how to calculate phenotypic variance explained

Issue - State: closed - Opened by carrot881216 8 months ago - 1 comment

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

Issue - State: closed - Opened by Jorge-Hernansanz 9 months ago - 5 comments

#44 - Calculate heritability

Issue - State: closed - Opened by snowformatics 9 months ago - 2 comments

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

Issue - State: closed - Opened by vb-iman 9 months ago - 3 comments

#42 - warpedlmm installation

Issue - State: closed - Opened by asifzubair 9 months ago - 2 comments

#41 - TypeError in flutil.manhattan_plot()

Issue - State: closed - Opened by vb-iman 9 months ago - 7 comments

#40 - AttributeError; scipy vs numpy in utils

Issue - State: closed - Opened by vb-iman 10 months ago - 6 comments

#39 - PValue Output Format

Issue - State: closed - Opened by snowformatics 10 months ago - 16 comments

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

Issue - State: closed - Opened by snowformatics 12 months ago - 13 comments

#37 - Unable to run with multiple phenotypic traits together

Issue - State: closed - Opened by jefflllyyy about 1 year ago - 1 comment

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

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

#35 - ValueError: No individual observed for the SNP

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

#34 - FloatingPointError: divide by zero encountered in true_divide

Issue - State: closed - Opened by zhaouu about 2 years ago - 3 comments

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

Issue - State: closed - Opened by yyang-peko about 2 years ago - 1 comment

#32 - Support cbgen>=1.0.1

Pull Request - State: closed - Opened by ofrei over 2 years ago - 4 comments

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

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

#30 - Run without PLINK format

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

#29 - epistatis test error

Issue - State: closed - Opened by snowformatics almost 3 years ago - 8 comments

#28 - Hapmap format

Issue - State: closed - Opened by snowformatics almost 3 years ago - 2 comments

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

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

#25 - Scaling of beta estimates with case control analyses

Issue - State: closed - Opened by CSGallagher almost 3 years ago - 2 comments

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

Issue - State: closed - Opened by CSGallagher almost 3 years ago - 2 comments

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

Pull Request - State: closed - Opened by code-review-doctor almost 3 years ago - 1 comment

#22 - Some tests are skipped due to duplicate names

Issue - State: closed - Opened by code-review-doctor almost 3 years ago - 1 comment

#20 - Issue with multiple phenotype files

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

#18 - Installing fast-lmm on CentOS 7

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

#17 - ValueError: No objects to concatenate

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

#16 - Epistatic interaction coefficient and error

Issue - State: closed - Opened by edinburgh-biomedical-ai almost 4 years ago - 5 comments

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

Pull Request - State: open - Opened by lucasmiranda42 almost 4 years ago

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

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

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

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

#12 - LMM.getPosteriorWeights() returns inconsitent results

Issue - State: closed - Opened by remomomo about 4 years ago - 3 comments

#11 - GenDist is NaN after running single_snp analysis

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

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

Issue - State: closed - Opened by remomomo about 4 years ago - 1 comment

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

Issue - State: closed - Opened by limin321 about 4 years ago - 3 comments

#8 - Installation problems on Windwos10

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

#7 - Adding ubuntu docker build + instructions

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

#5 - How to generate the input file

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

#4 - How fastlmm deal with "NA" in covariate file?

Issue - State: closed - Opened by baolichang almost 5 years ago - 3 comments

#3 - Add unit test for #2

Pull Request - State: closed - Opened by gaow almost 5 years ago - 1 comment

#2 - Fix Laplace and EP GLMM when K is available but G is not set

Pull Request - State: closed - Opened by gaow almost 5 years ago - 1 comment

#1 - fast lmm python

Issue - State: closed - Opened by DesmondSmith about 5 years ago - 10 comments