Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / chr1swallace/coloc issues and pull requests

#182 - Would the number of SNPs in input impact the result for the same SNP?

Issue - State: open - Opened by zhuxxyy12 about 2 months ago - 1 comment

#181 - coloc.abf question: PP.H3.abf=1 and small PP.H4.abf

Issue - State: open - Opened by zhuxxyy12 2 months ago

#180 - Issue for minimum p value

Issue - State: open - Opened by LidaWangPSU 3 months ago - 3 comments

#179 - If immunochip summary data can be used for coloc analysis?

Issue - State: open - Opened by Davidseye 3 months ago - 2 comments

#177 - Is claudia.R the main code for coloc.abf?

Issue - State: open - Opened by jielab 3 months ago

#176 - subset_dataset function

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

#174 - Unusual hypothesis priors when using coloc.abf() ?

Issue - State: open - Opened by HarrietRB 4 months ago

#173 - whether COLOC analysis require CHR and BP information

Issue - State: open - Opened by tss0222 5 months ago - 1 comment

#172 - Question about Constant Values in r.df2 Column of Coloc Output

Issue - State: open - Opened by Xenophong 5 months ago - 8 comments

#167 - Add the ability to use variant-specific prior probabilities

Pull Request - State: closed - Opened by jeffreypullin 8 months ago

#166 - error for coloc input datacheck

Issue - State: open - Opened by forevertl 8 months ago - 2 comments

#164 - Update susie.R to retain dimnames in single-variant edge-case

Pull Request - State: closed - Opened by cfbeuchel 9 months ago - 3 comments

#163 - runsusie() error with convergence

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

#160 - Error in coloc.susie ()

Issue - State: open - Opened by Huiflorazhan 10 months ago - 2 comments

#158 - NULL Result from coloc.susie

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

#155 - Add new_file.txt

Pull Request - State: closed - Opened by ramin777777 11 months ago - 2 comments

#154 - corrected credible.sets function for top SNP

Pull Request - State: closed - Opened by GRealesM 11 months ago

#153 - added function to extract credible sets

Pull Request - State: closed - Opened by GRealesM 11 months ago

#152 - Added credible sets function

Pull Request - State: closed - Opened by GRealesM 11 months ago

#151 - How to interpret the results of susie summary？

Issue - State: open - Opened by Leweibo 11 months ago - 3 comments

#150 - The pre-process of QTL-GWAS colocalisation

Issue - State: open - Opened by ttongyyang 11 months ago - 3 comments

#149 - "cc" and "quant" variables effect size

Issue - State: closed - Opened by ariadnacilleros 11 months ago - 2 comments

#148 - Add quiet=FALSE to coloc.abf()

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

#147 - coloc.susie returns NA results without error message

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

#146 - [Question] Calculating coloc.abf PP.H4.abf

Issue - State: closed - Opened by ctat41 about 1 year ago

#145 - Error when running `check_dataset()`

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

#144 - Add website to DESCRIPTION

Pull Request - State: closed - Opened by olivroy about 1 year ago

#143 - Add check for infinite values in beta/varbeta

Pull Request - State: closed - Opened by jeffreypullin about 1 year ago

#142 - runsusie and susieR results differ

Issue - State: open - Opened by maguileraf about 1 year ago - 8 comments

#141 - coloc.abf error

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

#138 - description errors

Issue - State: open - Opened by mocksu over 1 year ago

#137 - Summary stats of two traits are from the same dataset

Issue - State: closed - Opened by Sheeya-Dong over 1 year ago - 6 comments

#136 - XtX is not symmetric

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

#135 - Error when running check_dataset

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

#134 - Add RStudio related files

Pull Request - State: closed - Opened by jeffreypullin over 1 year ago - 2 comments

#133 - Error if beta and/or varbeta contain `Inf`

Issue - State: closed - Opened by oborisov over 1 year ago - 5 comments
Labels: enhancement

#132 - LD matrix on SuSIE_coloc

Issue - State: closed - Opened by Zhangzzzzzy over 1 year ago - 7 comments

#131 - coloc.abf

Issue - State: open - Opened by MoMaz123 over 1 year ago - 1 comment

#130 - Question on "First: select the SNPs to study."

Issue - State: open - Opened by anbai106 over 1 year ago

#128 - error in check_dataset: duplicated SNPs

Issue - State: open - Opened by PyunJung-Min over 1 year ago - 4 comments

#127 - length of snp vector should be 1 less than ncol(res$lbf_variable)

Issue - State: open - Opened by shannjiang over 1 year ago - 6 comments

#125 - object 'LD' not found in installation (build_vignettes=TRUE)

Issue - State: open - Opened by bbb801 over 1 year ago - 4 comments

#124 - Query about eQTL summary selection for coloc analysis

Issue - State: open - Opened by TaoShiyue over 1 year ago

#123 - GWAS-GWAS colocalisation

Issue - State: open - Opened by Liuyh275 over 1 year ago - 6 comments

#119 - Sample size (N or n) not recognised by coloc.susie

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

#117 - Error when running COLOC

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

#116 - Questions about the coloc hypotheses

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

#115 - How to construct a dataset for coloc analysis?

Issue - State: closed - Opened by mocksu almost 2 years ago - 6 comments

#114 - Colocalization of eQTL and GWAS

Issue - State: open - Opened by cy6n about 2 years ago - 5 comments

#113 - Using coloc for conditionally independent eQTLs in the HLA region

Issue - State: open - Opened by joycekang about 2 years ago - 3 comments

#112 - Interpretation on SNP.PP.H4

Issue - State: open - Opened by zl2860 about 2 years ago - 2 comments

#111 - coloc.abf result: unexpectedly high PP.H4.abf

Issue - State: open - Opened by QingningWang2022 about 2 years ago - 4 comments

#110 - Results from coloc.abf

Issue - State: open - Opened by Duhh56 about 2 years ago - 3 comments

#108 - Varbeta for eQTL and GWAS dataset

Issue - State: closed - Opened by HKJ396 about 2 years ago - 5 comments

#107 - N argument missing when calling susieR::susie_rss()

Issue - State: open - Opened by AMCalejandro about 2 years ago - 20 comments

#106 - Bug in code to set up sample size argument to pass to susie_rss

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

#105 - res$summary shows PP.H2.abf=1 AND PP.H4.abf=1

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

#103 - coloc.susie: warning about providing sample size

Issue - State: closed - Opened by nshrine over 2 years ago - 7 comments

#102 - Question about sdY

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

#101 - MAF score from GWAS results using COLOC.susie as well as LD matrix question

Issue - State: closed - Opened by HKJ396 over 2 years ago - 12 comments

#99 - PP global H4 vs PP snp H4

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

#98 - How to interpret coloc.susie results with two different variants in low LD?

Issue - State: closed - Opened by wonjikim11 over 2 years ago - 6 comments

#97 - Output returns NaN

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

#96 - Error when using coloc 5.2.0 version

Issue - State: closed - Opened by JFF1594032292 over 2 years ago - 11 comments

#95 - coloc.signals with 'cond' method is nto working properly

Issue - State: closed - Opened by npirastu over 2 years ago - 7 comments

#94 - Runsusie returns null credible set

Issue - State: closed - Opened by jeji0209 over 2 years ago - 6 comments

#93 - HLA imputation and SUSIE

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

#92 - Error installing coloc

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

#90 - runsusie: taking too much iterations to reach convegence

Issue - State: closed - Opened by zillurbmb51 over 2 years ago - 9 comments

#89 - Issue with plotting

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

#88 - Run coloc.abf for multiple loci together with for loop or other alternatives

Issue - State: closed - Opened by zillurbmb51 almost 3 years ago - 3 comments

#87 - How to get gene level H4?

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

#86 - Error while running moloc

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

#85 - How to find H0 to H3 from the coloc.abf output for each snp

Issue - State: closed - Opened by zillurbmb51 almost 3 years ago - 1 comment

#83 - coloc.abf with eQTLgen and GWAS data errors

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

#82 - coloc.detail, coloc.process function not found (coloc 5.1.2)

Issue - State: open - Opened by zillurbmb51 almost 3 years ago - 5 comments
Labels: bug

#81 - Preparing data for 'CC' and 'quant' traits, tried but getting error

Issue - State: closed - Opened by zillurbmb51 almost 3 years ago - 10 comments