Ecosyste.ms: Issues

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

GitHub / FoxoTech/methylprep issues and pull requests

#132 - Code needs to be updated for Illumina MethylationEPIC-8 v2.0 arrays

Issue - State: open - Opened by petermchale 16 days ago - 2 comments

#131 - methylize diff_meth_regions throwing an error

Issue - State: open - Opened by harshaa10 6 months ago

#129 - Any groups for exchange?

Issue - State: open - Opened by Shahin-rmz about 1 year ago

#127 - adapted code for pandas2.0

Pull Request - State: open - Opened by gilgameshjw over 1 year ago - 8 comments

#126 - Bump certifi from 2022.6.15 to 2023.7.22

Pull Request - State: open - Opened by dependabot[bot] over 1 year ago
Labels: dependencies

#124 - Bump scipy from 1.8.0 to 1.10.0

Pull Request - State: open - Opened by dependabot[bot] over 1 year ago
Labels: dependencies

#122 - Analysing Infinium MethylationEPIC v2.0 Kit already implemented?

Issue - State: open - Opened by claus-h-g over 1 year ago - 8 comments

#121 - Bump requests from 2.27.1 to 2.31.0

Pull Request - State: open - Opened by dependabot[bot] over 1 year ago
Labels: dependencies

#120 - [Snyk] Security upgrade tornado from 6.2 to 6.3.2

Pull Request - State: open - Opened by jfechner-foxo over 1 year ago

#119 - copy number

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

#118 - Bump setuptools from 63.1.0 to 65.5.1

Pull Request - State: open - Opened by dependabot[bot] almost 2 years ago
Labels: dependencies

#117 - Bump certifi from 2022.6.15 to 2022.12.7

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago - 1 comment
Labels: dependencies

#116 - How to control filtering in command line

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

#115 - Feature/v1.7.1

Pull Request - State: closed - Opened by marcmaxson over 2 years ago

#114 - Feature/v1.7.0 -- adds parquet support

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

#113 - Bump lxml from 4.7.1 to 4.9.1

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago
Labels: dependencies

#112 - incorp Mauro's updates (pNegECDF and infer switch) into v1.7.0

Pull Request - State: closed - Opened by marcmaxson over 2 years ago - 1 comment

#110 - Adapting sample_sheets.py to Windows users

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

#109 - Addition of negative control based pvalue calculation

Pull Request - State: closed - Opened by notmaurox over 2 years ago

#108 - Feature/v1.6.3

Pull Request - State: closed - Opened by marcmaxson over 2 years ago - 1 comment

#107 - Update pOOBAH pval calculation

Pull Request - State: closed - Opened by notmaurox over 2 years ago

#106 - custom manifest support

Pull Request - State: open - Opened by notmaurox over 2 years ago

#105 - minor bug fixes

Pull Request - State: closed - Opened by marcmaxson over 2 years ago - 1 comment

#104 - Control of output file location/names

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

#103 - Feature/v1.6.1

Pull Request - State: closed - Opened by marcmaxson almost 3 years ago - 1 comment

#102 - Accessing probe intensities for QC metrics

Issue - State: closed - Opened by notmaurox almost 3 years ago

#101 - Manifest

Issue - State: open - Opened by stefdecondor31 almost 3 years ago - 3 comments

#100 - CLI does not import the right module

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

#99 - RFE: Allow to specify output directory of methylprep-cli

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

#98 - Feature/v1.6.0

Pull Request - State: closed - Opened by marcmaxson about 3 years ago

#97 - Feature/v1.5.8

Pull Request - State: closed - Opened by marcmaxson about 3 years ago

#96 - Feature/v1.5.7 -- unlocks pandas (v 1.3.0+ supported now)

Pull Request - State: closed - Opened by marcmaxson about 3 years ago

#95 - feature/v1.5.6 and feature/v1.5.5-docs

Pull Request - State: closed - Opened by marcmaxson about 3 years ago

#94 - Feature/v1.5.5 docs

Pull Request - State: closed - Opened by marcmaxson about 3 years ago

#93 - Feature/v1.5.5 docs

Pull Request - State: closed - Opened by marcmaxson about 3 years ago

#92 - Feature/v1.5.5

Pull Request - State: closed - Opened by marcmaxson about 3 years ago

#91 - Feature/v1.5.3

Pull Request - State: closed - Opened by marcmaxson over 3 years ago

#90 - download support TAR of BED files too

Issue - State: open - Opened by marcmaxson over 3 years ago - 1 comment
Labels: enhancement

#89 - Feature/v1.5.2

Pull Request - State: closed - Opened by marcmaxson over 3 years ago

#88 - patch to help read_geo_processed.py detect txt csv files better

Pull Request - State: closed - Opened by marcmaxson over 3 years ago

#87 - Feature/v1.5.0

Pull Request - State: closed - Opened by marcmaxson over 3 years ago

#86 - Bump urllib3 from 1.26.4 to 1.26.5

Pull Request - State: closed - Opened by dependabot[bot] over 3 years ago
Labels: dependencies

#84 - Feature/v1.4.6

Pull Request - State: closed - Opened by marcmaxson over 3 years ago

#83 - Feature/v1.4.4

Pull Request - State: closed - Opened by marcmaxson over 3 years ago

#82 - Feature/v1.4.2 huber debug

Pull Request - State: closed - Opened by marcmaxson over 3 years ago

#81 - Feature/v1.4.2

Pull Request - State: closed - Opened by marcmaxson over 3 years ago - 1 comment

#80 - Feature/v1.4.2

Pull Request - State: closed - Opened by marcmaxson over 3 years ago

#79 - Feature/v1.4.0 bugs

Pull Request - State: closed - Opened by marcmaxson over 3 years ago

#78 - Feature/v1.4.0 sesame

Pull Request - State: closed - Opened by marcmaxson over 3 years ago

#77 - Feature/v1.4.0 sesame

Pull Request - State: closed - Opened by marcmaxson over 3 years ago

#76 - Feature/v1.3.3

Pull Request - State: closed - Opened by marcmaxson almost 4 years ago - 2 comments

#75 - Feature/v1.3.3

Pull Request - State: closed - Opened by marcmaxson almost 4 years ago

#74 - bug fix

Pull Request - State: closed - Opened by marcmaxson almost 4 years ago

#73 - Feature/v1.3.1

Pull Request - State: closed - Opened by marcmaxson about 4 years ago

#72 - Feature/v1.3.1

Pull Request - State: closed - Opened by marcmaxson about 4 years ago

#71 - retain compressed idat.gz files in pipeline and download

Pull Request - State: closed - Opened by marcmaxson about 4 years ago

#70 - Revert "Allow processing IDAT files without decompression"

Pull Request - State: closed - Opened by marcmaxson about 4 years ago

#69 - offer Apache Arrow output option in methylprep.run_pipeline -- ideal for GPU machine learning use case

Issue - State: closed - Opened by marcmaxson about 4 years ago - 2 comments
Labels: enhancement

#68 - Allow processing IDAT files without decompression

Pull Request - State: closed - Opened by adamritter about 4 years ago

#66 - Int64 allows NAs while it makes pd.merge more efficient

Pull Request - State: closed - Opened by adamritter about 4 years ago - 3 comments

#65 - Close FTP before unpacking files

Pull Request - State: closed - Opened by adamritter about 4 years ago

#64 - Close tar file before trying to delete it

Pull Request - State: closed - Opened by adamritter about 4 years ago

#63 - Speed up methylation data reading/processing

Pull Request - State: closed - Opened by adamritter about 4 years ago

#62 - run_pipeline(); change default behavior to return None instead of list of data_containers/beta_values to save memory.

Issue - State: closed - Opened by marcmaxson over 4 years ago - 1 comment
Labels: enhancement, Priority: Short-term

#61 - Methylprep doesn't process mixed data (EPIC + 450k) sets yet

Issue - State: closed - Opened by marcmaxson over 4 years ago - 3 comments
Labels: bug

#59 - poobah pkl file is not generated

Issue - State: closed - Opened by moranr7 over 4 years ago - 2 comments
Labels: bug, enhancement

#58 - methylprep -all - batch-size memory does not clear between batches

Issue - State: closed - Opened by marcmaxson over 4 years ago - 1 comment
Labels: bug, Priority: Short-term

#57 - methylprep.read_geo exceptions

Issue - State: open - Opened by marcmaxson over 4 years ago
Labels: enhancement

#56 - Dev --> Master (#55)

Pull Request - State: closed - Opened by marcmaxson over 4 years ago

#55 - Dev --> Master

Pull Request - State: closed - Opened by marcmaxson over 4 years ago

#54 - Dev (updating the __version__ part)

Pull Request - State: closed - Opened by marcmaxson over 4 years ago

#53 - Feature/mouse

Pull Request - State: closed - Opened by marcmaxson over 4 years ago

#52 - v1.2.6

Pull Request - State: closed - Opened by marcmaxson over 4 years ago

#51 - save_control only works with single batches

Issue - State: open - Opened by marcmaxson over 4 years ago
Labels: enhancement

#50 - ModuleNotFoundError: No module named 'methylcheck.probes'

Issue - State: closed - Opened by moqri over 4 years ago - 3 comments
Labels: bug

#49 - readthedocs autodocs autosummary

Pull Request - State: closed - Opened by marcmaxson over 4 years ago

#48 - v1.2.4 unit test fix

Pull Request - State: closed - Opened by marcmaxson over 4 years ago

#47 - v1.2.4 (with --all CLI option and higher-performance file output)

Pull Request - State: closed - Opened by marcmaxson over 4 years ago

#46 - v1.2.3 big fixes

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

#45 - v.1.2.2 minor documentation improvements

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

#44 - Add download command example in the README

Issue - State: closed - Opened by haa-gg almost 5 years ago - 1 comment
Labels: documentation

#43 - load_processed function: enable it to create dataframe of betas from processed csvs

Issue - State: closed - Opened by marcmaxson almost 5 years ago - 1 comment
Labels: bug

#42 - v1.2.2 added --save_control CLI option

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

#40 - Feature/composite

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

#39 - Feature/composite

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

#38 - v1.2.0 feature/geometa tested and ready to release

Pull Request - State: closed - Opened by marcmaxson about 5 years ago

#37 - Feature/geometa

Pull Request - State: closed - Opened by marcmaxson about 5 years ago

#36 - GEO downloader doesn't handle "TAR (of TXT)" of files, only "TAR (of IDAT)" files.

Issue - State: closed - Opened by marcmaxson about 5 years ago - 1 comment
Labels: enhancement, wontfix, Priority: Long-term

#35 - Minor bug fixes, and coveralls stopped working

Pull Request - State: closed - Opened by marcmaxson about 5 years ago

#34 - Create samplesheet from MINiML file, without processing or downloading

Issue - State: closed - Opened by marcmaxson about 5 years ago - 1 comment
Labels: enhancement, Priority: Short-term

#33 - RUVm (postprocessing method to reduce batch effects)

Issue - State: open - Opened by marcmaxson about 5 years ago - 1 comment
Labels: enhancement, Priority: Long-term

#32 - v1.1.9 bug fix

Pull Request - State: closed - Opened by marcmaxson about 5 years ago