Ecosyste.ms: Issues

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

GitHub / hansenlab/minfi issues and pull requests

#278 - Repressing question using minfi

Issue - State: open - Opened by demis001 3 months ago

#277 - Problem with qcPlot axes

Issue - State: closed - Opened by VasLem 4 months ago - 1 comment

#276 - Galaxy Wrapper code repository

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

#274 - EPIC v2 preprocessQuantile()

Issue - State: open - Opened by psychesha21 7 months ago

#273 - detectionP broken as of latest matrixStats update

Issue - State: closed - Opened by yhoogstrate 7 months ago

#272 - EPIC V2 to EPIC V1

Issue - State: open - Opened by PierreSolomon 7 months ago - 12 comments

#271 - Changes for EPICv2

Pull Request - State: closed - Opened by jmacdon 7 months ago

#270 - Loading minfi on MacOS

Issue - State: closed - Opened by mehmet-cay 7 months ago - 7 comments

#268 - EPIC v2.0 - preprocessIllumina returning error

Issue - State: open - Opened by chanmur 8 months ago - 3 comments

#267 - Error encounter during EPIC methylation analysis

Issue - State: open - Opened by sarah91-RA 8 months ago - 4 comments

#266 - EstimateCellCounts with EPIC V2 data

Issue - State: open - Opened by kimberzhu 9 months ago - 1 comment

#265 - Fixes selection of probes by type in preprocessNoob.

Pull Request - State: closed - Opened by jonathonl 9 months ago - 1 comment

#264 - preprocessNoob using incorrect row indices to Meth and Unmeth matrices

Issue - State: open - Opened by jonathonl 9 months ago - 10 comments

#263 - Custom minfi manifest and annotation packages

Issue - State: open - Opened by dancingRNA 10 months ago

#261 - how to combine EPIC and EPIC2 array data?

Issue - State: open - Opened by aa20g217 10 months ago - 4 comments

#260 - Problem in qcReport

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

#259 - Fixing cpgCollapse bug

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

#258 - Problem with preprocessIllumina

Issue - State: closed - Opened by Zszywek 12 months ago - 5 comments

#257 - getUnMeth() didn't work for EPIC v2

Issue - State: open - Opened by atomnh 12 months ago - 2 comments

#256 - Upcoming change to DelayedArray::realize()

Issue - State: closed - Opened by hpages 12 months ago - 7 comments

#253 - lm.fit Error during preprocessFunnorm for EPIC V2 array

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

#252 - Compatibility with Illumina Mouse Array and EPIC Version 2

Pull Request - State: open - Opened by chiaraherzog about 1 year ago

#250 - Error I preprocess quantile

Issue - State: open - Opened by simonjuleseric2 over 1 year ago

#248 - read.metharray.sheet Basename issue

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

#247 - Custom Manifest

Issue - State: open - Opened by demis001 over 1 year ago

#246 - batch correction using control probe

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

#245 - Illumina Mouse Methylation Array Annotation into minfi

Issue - State: open - Opened by edco84 over 1 year ago

#244 - Whether the minfi can analzye Infinium EPIC V2 product?

Issue - State: open - Opened by AliceCheng7 over 1 year ago - 1 comment

#242 - Update estimateCellCounts.R

Pull Request - State: closed - Opened by metamaden almost 2 years ago

#240 - Support for EPIC v2.0 arrays?

Issue - State: open - Opened by karoliskoncevicius about 2 years ago - 9 comments

#239 - preprocessFunnorm: Error in kmeans (initial centers are not distinct)

Issue - State: open - Opened by mikldk about 2 years ago - 7 comments

#238 - Error with bumphunter during p-value estimation

Issue - State: open - Opened by alex-d13 about 2 years ago - 1 comment

#237 - Always showing "blood" in meanPlot even for DLPFC mixture

Issue - State: open - Opened by randel about 2 years ago - 1 comment

#236 - Installation Error on RStudio Cloud

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

#235 - Analyse Data from GEO with minfi

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

#234 - Can't download minfi with the recomended BiocManager

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

#233 - 27k array issue with preprocess

Issue - State: open - Opened by biostars-nyc over 2 years ago

#232 - hg38

Issue - State: open - Opened by etiennedanis over 2 years ago - 4 comments

#231 - Bug in densityBeanPlot function

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

#230 - BUG: *** caught segfault ***

Issue - State: open - Opened by DUAN-GAO over 2 years ago

#229 - Error in preprocessNoob(RGset, verbose=10) - script killed

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

#228 - meanPlot in EstimateCellCounts2 and batch effects

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

#226 - Can't read IDAT with this error.

Issue - State: open - Opened by kwanghoon821 about 3 years ago

#224 - [Issue] Unable to load manifest package?

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

#223 - Incomplete User Guide

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

#222 - Cell count proportions sum more than 1

Issue - State: open - Opened by ponche-de-kiwi over 3 years ago

#221 - Bumphunter statistical stringency

Issue - State: open - Opened by gremame over 3 years ago

#220 - preprocessQuantile getSex error: -Inf median CN

Issue - State: open - Opened by zxl124 over 3 years ago - 1 comment

#219 - Supporting new species?

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

#218 - Warnings when reading data

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

#217 - estimateCellCounts fails with IlluminaHumanMethylationEPIC

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

#216 - Made preprocessFunnorm() respect verbose=FALSE

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

#214 - gaphunter errors for input class matrix

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

#213 - read.metharray.exp function doesn't work

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

#212 - Which dbSNP build is used in the getSnpInfo function

Issue - State: closed - Opened by nikolayaivanov over 4 years ago

#209 - Green and Red columns inverted in controlStripPlot

Issue - State: open - Opened by MGiulia over 4 years ago - 1 comment

#207 - HDF5: Expose read_metharray2

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

#206 - HDF5: Refactor annotation design

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

#205 - HDF5: Make HDF5 stubs in code

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

#204 - HDF5: Setup HDF5 testing

Issue - State: open - Opened by kasperdanielhansen over 4 years ago - 7 comments

#203 - minfi user guide query

Issue - State: open - Opened by prasundutta87 over 4 years ago

#202 - getAnnotation() details

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

#201 - Error in `preprocessFunnorm`

Issue - State: open - Opened by kdkorthauer over 4 years ago - 9 comments

#200 - Error with normalization

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

#199 - Discrepancy in number of probes

Issue - State: open - Opened by VilainLab almost 5 years ago

#197 - Issue loading target files

Issue - State: closed - Opened by VilainLab almost 5 years ago - 2 comments

#196 - Memory usage by makeGenomicRatioSetFromMatrix

Issue - State: closed - Opened by timpeters82 almost 5 years ago - 4 comments

#194 - Incorporate Bayesian measurement error procedure into estimateCellCounts

Pull Request - State: open - Opened by sandrews5 about 5 years ago - 2 comments

#193 - minfi objects declare <Object with null pointer> in Rstudio

Issue - State: closed - Opened by wudustan about 5 years ago - 1 comment

#192 - How can I subset a GenomicRatioSet?

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

#191 - Error FlowSortedBloodEPIC on a cluster

Issue - State: open - Opened by EPICuser1 about 5 years ago - 1 comment

#190 - How can I specify the number of columns for the legend in densityPlot?

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

#189 - cpgCollapse bugfix

Pull Request - State: closed - Opened by rafalab over 5 years ago

#188 - Loss of probes during preprocessIllumina

Issue - State: open - Opened by LambertDorssers over 5 years ago - 6 comments

#187 - CordBlood

Issue - State: open - Opened by demis001 over 5 years ago

#186 - error in minfi dmpFinder

Issue - State: closed - Opened by hope2003 over 5 years ago - 1 comment

#185 - estimateCellCounts error

Issue - State: closed - Opened by ruizhang3333 over 5 years ago - 4 comments

#184 - .cpgCollapse’ for signature ‘"data.frame"

Issue - State: open - Opened by yeswzc over 5 years ago

#183 - makeGenomicRatioSetFromMatrix function for EPIC data?

Issue - State: open - Opened by priyatamapandey over 5 years ago - 1 comment

#182 - getProbeType return different length of probe types

Issue - State: open - Opened by ShannonSzeto over 5 years ago - 7 comments

#181 - Error with `getAnnotation`

Issue - State: closed - Opened by LiNk-NY over 5 years ago - 2 comments

#180 - Error in preprocessQuantile and preprocessFunnorm

Issue - State: open - Opened by michaelnoe almost 6 years ago - 5 comments