hansenlab/minfi issues and pull requests

#275 - Error while reading the data using (read.metharray.exp)

Issue - State: open - Opened by royamani about 1 month ago

#274 - EPIC v2 preprocessQuantile()

Issue - State: open - Opened by psychesha21 about 2 months ago

#273 - detectionP broken as of latest matrixStats update

Issue - State: closed - Opened by yhoogstrate 2 months ago

#272 - EPIC V2 to EPIC V1

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

#271 - Changes for EPICv2

Pull Request - State: closed - Opened by jmacdon 3 months ago

#270 - Loading minfi on MacOS

Issue - State: closed - Opened by mehmet-cay 3 months ago - 7 comments

#269 - Construct RGChannelSet object from raw methylated and raw unmethylated csv files

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

#268 - EPIC v2.0 - preprocessIllumina returning error

Issue - State: open - Opened by chanmur 3 months ago - 1 comment

#267 - Error encounter during EPIC methylation analysis

Issue - State: open - Opened by sarah91-RA 3 months ago - 4 comments

#266 - EstimateCellCounts with EPIC V2 data

Issue - State: open - Opened by kimberzhu 4 months ago - 1 comment

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

Pull Request - State: closed - Opened by jonathonl 4 months ago - 1 comment

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

Issue - State: open - Opened by jonathonl 4 months ago - 9 comments

#263 - Custom minfi manifest and annotation packages

Issue - State: open - Opened by dancingRNA 5 months ago

#262 - preprocessSWAN fails to normalize RGChannelSet

Issue - State: open - Opened by alexandernassar24 6 months ago

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

Issue - State: open - Opened by aa20g217 6 months ago - 4 comments

#260 - Problem in qcReport

Issue - State: open - Opened by lilwo 6 months ago - 2 comments

#259 - Fixing cpgCollapse bug

Pull Request - State: closed - Opened by rafalab 6 months ago

#258 - Problem with preprocessIllumina

Issue - State: closed - Opened by Zszywek 7 months ago - 5 comments

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

Issue - State: open - Opened by atomnh 7 months ago - 2 comments

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

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

#255 - How to analyze A/B compartment after using liftOver function to annotate hg38

Issue - State: open - Opened by h20gg702 8 months ago

#254 - combine EPIC and EPICv2 array leads to less than 200k of probes remained

Issue - State: closed - Opened by yeswzc 8 months ago

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

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

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

Pull Request - State: open - Opened by chiaraherzog 10 months ago

#251 - No IDAT files with both Red and Green channel were found (IDAT files named 'red' and 'grn' instead of 'Red' and 'Grn')

Issue - State: closed - Opened by Manoswini-02 11 months ago - 5 comments

#250 - Error I preprocess quantile

Issue - State: open - Opened by simonjuleseric2 12 months ago

#249 - Error in get(referencePkg): object 'FlowSorted.Blood.EPIC' not found

Issue - State: open - Opened by yr542 12 months ago

#248 - read.metharray.sheet Basename issue

Issue - State: open - Opened by keeblee 12 months ago

#247 - Custom Manifest

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

#246 - batch correction using control probe

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

#245 - Illumina Mouse Methylation Array Annotation into minfi

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

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

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

#243 - wrong probe types used for EPIC samples in `preprocessNoob` due to b2-based manifest and b4-based annotation

Issue - State: open - Opened by maximilian-leitheiser over 1 year ago

#242 - Update estimateCellCounts.R

Pull Request - State: closed - Opened by metamaden over 1 year ago

#241 - Error in `cpgCollapse` if the `GenomicRatioSet` doesn't have any copy number values

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

#240 - Support for EPIC v2.0 arrays?

Issue - State: open - Opened by karoliskoncevicius over 1 year ago - 9 comments

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

Issue - State: open - Opened by mikldk over 1 year ago - 7 comments

#238 - Error with bumphunter during p-value estimation

Issue - State: open - Opened by alex-d13 over 1 year ago - 1 comment

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

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

#236 - Installation Error on RStudio Cloud

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

#235 - Analyse Data from GEO with minfi

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

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

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

#233 - 27k array issue with preprocess

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

#232 - hg38

Issue - State: open - Opened by etiennedanis almost 2 years ago - 1 comment

#231 - Bug in densityBeanPlot function

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

#230 - BUG: * caught segfault *

Issue - State: open - Opened by DUAN-GAO about 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

#227 - Does minfi support Infinium Mouse Methylation BeadChip Array data?

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

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

Issue - State: open - Opened by kwanghoon821 over 2 years ago

#225 - Specify one or multiple directories for idat files other than the base directory of the samplesheet (read.metharray.sheet).

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

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

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

#223 - Incomplete User Guide

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

#222 - Cell count proportions sum more than 1

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

#221 - Bumphunter statistical stringency

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

#220 - preprocessQuantile getSex error: -Inf median CN

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

#219 - Supporting new species?

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

#218 - Warnings when reading data

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

#217 - estimateCellCounts fails with IlluminaHumanMethylationEPIC

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

#216 - Made preprocessFunnorm() respect verbose=FALSE

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

#215 - A/B compartment agreement across array platforms (450k and EPIC) and multiple datasets

Issue - State: open - Opened by santanalele over 3 years ago - 2 comments

#214 - gaphunter errors for input class matrix

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

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

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

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

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

#211 - Error in creating RGSet using read.metharray.exp function in R

Issue - State: closed - Opened by kendrix10 about 4 years ago

#210 - query regarding manifest/annotation file and trouble creating new manifest object

Issue - State: open - Opened by prasundutta87 about 4 years ago - 3 comments

#209 - Green and Red columns inverted in controlStripPlot

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

#208 - query regarding using manifest and annotation in Minfi (EPIC Methylation array analysis)

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

#207 - HDF5: Expose read_metharray2

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

#206 - HDF5: Refactor annotation design

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

#205 - HDF5: Make HDF5 stubs in code

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

#204 - HDF5: Setup HDF5 testing

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

#203 - minfi user guide query

Issue - State: open - Opened by prasundutta87 about 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 - 8 comments

#200 - Error with normalization

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

#199 - Discrepancy in number of probes

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

#198 - preprocessIllumina function problem about bg.correct

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

#197 - Issue loading target files

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

#196 - Memory usage by makeGenomicRatioSetFromMatrix

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

#195 - Error in read.metharray(basenames = commonFiles, extended = extended, : [read.metharray] Trying to parse different IDAT files, of different size and type.

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

#194 - Incorporate Bayesian measurement error procedure into estimateCellCounts

Pull Request - State: open - Opened by sandrews5 over 4 years ago - 2 comments

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

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

#192 - How can I subset a GenomicRatioSet?

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

#191 - Error FlowSortedBloodEPIC on a cluster

Issue - State: open - Opened by EPICuser1 almost 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 almost 5 years ago - 2 comments

#189 - cpgCollapse bugfix

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

#188 - Loss of probes during preprocessIllumina

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

#187 - CordBlood

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

#186 - error in minfi dmpFinder

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

#185 - estimateCellCounts error

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

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

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

#179 - Normalization: Error in kmeans

Issue - State: open - Opened by royfrancis over 5 years ago - 8 comments

#178 - getBeta() long vectors not supported yet

Issue - State: open - Opened by stewart999 over 5 years ago - 8 comments

#177 - makeGenomicRatioSetFromMatrix function error?

Issue - State: open - Opened by alfonsosaera over 5 years ago - 2 comments

#176 - getGenomicRatioSetFromGEO failed!

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

GitHub / hansenlab/minfi issues and pull requests