Ecosyste.ms: Issues

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GitHub / epigenelabs/inmoose issues and pull requests

#81 - harmonize _isAllZero behavior on dataframes and ndarrays

Pull Request - State: open - Opened by EpigeneMax 3 days ago

#80 - Cr 421

Pull Request - State: open - Opened by EpigeneMax 4 days ago

#79 - Issue running ComBat-seq

Issue - State: open - Opened by richard-k-perez 8 days ago - 1 comment

#78 - Bump pypa/gh-action-pypi-publish from 1.9.0 to 1.10.1

Pull Request - State: closed - Opened by dependabot[bot] 11 days ago
Labels: dependencies

#77 - Bump pypa/gh-action-pypi-publish from 1.9.0 to 1.10.0

Pull Request - State: closed - Opened by dependabot[bot] 18 days ago - 1 comment
Labels: dependencies

#76 - allow arbitrary type for batch and group in `sim_rnaseq`

Pull Request - State: closed - Opened by EpigeneMax 21 days ago

#75 - lfcShrink() is not available in DEseq2

Issue - State: open - Opened by chenha0w 21 days ago - 1 comment

#74 - update numpy version constraint

Pull Request - State: closed - Opened by EpigeneMax 22 days ago

#73 - ensure meta-analysis is robust to NaN p-values

Pull Request - State: closed - Opened by EpigeneMax 22 days ago

#72 - fix array indexing bug

Pull Request - State: closed - Opened by EpigeneMax about 1 month ago

#71 - RunCombat for methylation arrays

Issue - State: open - Opened by brj0 about 1 month ago - 1 comment

#70 - Compilation error w/ gcc for early versions of inmoose

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

#69 - Release 0.7.1

Pull Request - State: closed - Opened by EpigeneMax 2 months ago

#68 - CR-355 improve documentation landing page

Pull Request - State: closed - Opened by EpigeneMax 2 months ago

#67 - CR-354 inform coveralls.io that our pipeline has parallel jobs

Pull Request - State: closed - Opened by EpigeneMax 2 months ago

#66 - CR-353 fix rendering of DEResults on readthedocs

Pull Request - State: closed - Opened by EpigeneMax 2 months ago

#65 - CR-352 fix a faulty constructor

Pull Request - State: closed - Opened by EpigeneMax 2 months ago

#64 - CR-219 add meta-analysis for differential expression

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

#63 - CR-305 harmonize diffexp results from limma

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

#62 - [CR-305] harmonizing diff exp results (edgepy part)

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

#61 - Warnings cleanup

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

#60 - CR-305 Use DataFrame for counts in DGEList

Pull Request - State: closed - Opened by EpigeneMax 3 months ago - 1 comment

#59 - Release 0.6.0

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

#58 - CR-309 compatibility with numpy 2.0.0

Pull Request - State: closed - Opened by EpigeneMax 3 months ago - 1 comment

#57 - Bump pypa/gh-action-pypi-publish from 1.8.14 to 1.9.0

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

#56 - Pythonize/Cythonize C++ code

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

#55 - bump version to 0.5.1

Pull Request - State: closed - Opened by EpigeneMax 4 months ago

#54 - fix row and columns name for dataframe

Pull Request - State: closed - Opened by Lea-Meunier 4 months ago

#53 - Release 0.5.0

Pull Request - State: closed - Opened by EpigeneMax 4 months ago

#52 - Use ruff to lint code

Pull Request - State: closed - Opened by EpigeneMax 4 months ago

#51 - Bump coverallsapp/github-action from 2.2.3 to 2.3.0

Pull Request - State: closed - Opened by dependabot[bot] 4 months ago
Labels: dependencies

#50 - Replaced logging module with a package logger variable

Pull Request - State: closed - Opened by VasLem 5 months ago - 3 comments

#49 - Provide a real logger and stop overriding the root one

Issue - State: closed - Opened by VasLem 5 months ago - 2 comments

#48 - CR-263 eBayes and topTable

Pull Request - State: closed - Opened by EpigeneMax 5 months ago

#47 - CR-263 contrasts-related functions from limma

Pull Request - State: closed - Opened by EpigeneMax 5 months ago

#46 - CR-263 duplicates from limma

Pull Request - State: closed - Opened by EpigeneMax 5 months ago

#45 - CR-263 lmfit functions from limma

Pull Request - State: closed - Opened by EpigeneMax 5 months ago

#44 - CR-263 tmixture functions

Pull Request - State: closed - Opened by EpigeneMax 5 months ago

#43 - add experimental support for MSVC

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

#42 - Add R-like functions for fitting linear models

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

#41 - Cleanup warnings

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

#40 - Using ComBat on transcript counts

Issue - State: open - Opened by VikArz02 6 months ago - 1 comment

#39 - fix ylim stability plot

Pull Request - State: closed - Opened by Lea-Meunier 7 months ago

#38 - Bump GitHub actions

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

#37 - Bump pypa/gh-action-pypi-publish from 1.8.6 to 1.8.11

Pull Request - State: closed - Opened by dependabot[bot] 8 months ago - 2 comments
Labels: dependencies

#36 - Bump actions/upload-artifact from 3 to 4

Pull Request - State: closed - Opened by dependabot[bot] 8 months ago - 2 comments
Labels: dependencies

#35 - Bump actions/download-artifact from 3 to 4

Pull Request - State: closed - Opened by dependabot[bot] 8 months ago - 2 comments
Labels: dependencies

#34 - Bump actions/setup-python from 4 to 5

Pull Request - State: closed - Opened by dependabot[bot] 8 months ago - 2 comments
Labels: dependencies

#33 - Bump actions/checkout from 3 to 4

Pull Request - State: closed - Opened by dependabot[bot] 8 months ago - 2 comments
Labels: dependencies

#32 - Support Python 3.12

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

#31 - Support Python 3.12

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

#30 - CR-154 setup workflow for coverage report

Pull Request - State: closed - Opened by EpigeneMax 8 months ago - 1 comment

#29 - fix documentation build

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

#28 - Improve check input message

Pull Request - State: closed - Opened by Lea-Meunier 8 months ago

#27 - [CR 151] port edgeR functions necessary for differential expression

Pull Request - State: closed - Opened by EpigeneMax 8 months ago - 1 comment

#26 - fix issue #25 and #10

Pull Request - State: closed - Opened by Lea-Meunier 9 months ago

#24 - port variance stabilizing transformation from DESeq2

Pull Request - State: closed - Opened by EpigeneMax 9 months ago

#23 - implement CR-133

Pull Request - State: closed - Opened by EpigeneMax 9 months ago

#22 - update reference of our pycombat article

Pull Request - State: closed - Opened by EpigeneMax 10 months ago

#21 - add verbose to consensus clustering computation

Pull Request - State: closed - Opened by guillaumeap 10 months ago

#20 - fix doc building on readthedocs.org

Pull Request - State: closed - Opened by EpigeneMax 10 months ago

#19 - Add pasilla and airway datasets to inmoose

Pull Request - State: closed - Opened by EpigeneMax 10 months ago

#18 - Add return single sample batch name when detected

Issue - State: closed - Opened by Lea-Meunier 10 months ago

#16 - Improve covariates use

Pull Request - State: closed - Opened by Lea-Meunier 11 months ago

#15 - Covariates data format in make_design_matrix

Issue - State: closed - Opened by Lea-Meunier 11 months ago

#14 - error with ref_batch due to incorrect slicing

Issue - State: open - Opened by alexandradanyi 11 months ago - 1 comment

#13 - raise ValueError if not a np ndarray (or pandas DataFrame)

Pull Request - State: closed - Opened by ceesu 12 months ago - 1 comment

#12 - Support LLP64 data model

Pull Request - State: open - Opened by EpigeneMax 12 months ago

#11 - compilation error with MSVC

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

#10 - reshape keep from pycombat_seq

Issue - State: closed - Opened by ceesu 12 months ago - 4 comments

#9 - port deseq2 to Python

Pull Request - State: closed - Opened by EpigeneMax almost 1 year ago - 2 comments

#8 - Add proper documentation to the data simulation module

Pull Request - State: closed - Opened by EpigeneMax almost 1 year ago

#7 - Consensus clustering

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

#6 - add RNASeq data simulation based on Splat model

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

#5 - Consensus Clustering

Issue - State: closed - Opened by soleneweill about 1 year ago - 1 comment
Labels: enhancement

#4 - NumPY RuntimeWarning: divide by zero encountered in true_divide

Issue - State: open - Opened by SantosRAC about 1 year ago - 3 comments

#3 - Documentation

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

#2 - pycombat module and function harmonization

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

#1 - CI/CD Github Actions

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