microbialgenomics-irsicaixaorg/dar issues and pull requests

#100 - [BIOCONDUCOR REVIEW / NAMWSPACE] `required_deps` seems to be an internal function and does not need to be exported.

Issue - State: closed - Opened by xec-cm about 1 year ago
Labels: bug

#99 - [BIOCONDUCTOR REVIEW / DESCRIPTION] Consider removing either the readr or the data.table dependency as they are both typically used for the same operation (read-in).

Issue - State: closed - Opened by xec-cm about 1 year ago
Labels: bug

#98 - [BIOCONDUCTOR REVIEW / DESCRIPTION] R version dependency should be 4.4.0 or higher

Issue - State: closed - Opened by xec-cm about 1 year ago
Labels: bug

#97 - [BUG] R CMD CHECK Warining on linux

Issue - State: closed - Opened by xec-cm about 1 year ago
Labels: bug

#96 - [BUG] R CMD BUILD warning

Issue - State: closed - Opened by xec-cm about 1 year ago
Labels: bug

#95 - [BUG] testhat read_data error with setequal

Issue - State: closed - Opened by xec-cm about 1 year ago
Labels: bug

#94 - closes #93

Pull Request - State: open - Opened by xec-cm over 1 year ago - 5 comments

#93 - [Feature Request] Try to extract stats with workflow-telemetry-action

Issue - State: closed - Opened by xec-cm over 1 year ago - 1 comment
Labels: enhancement

#92 - closes #91

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

#91 - [BUG] codecov badge from main to devel

Issue - State: closed - Opened by xec-cm over 1 year ago - 1 comment
Labels: bug

#90 - closes #89

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

#89 - [BUG] Convergence Issue in `corncob` when using `corncob::differentialTest()`

Issue - State: closed - Opened by xec-cm over 1 year ago - 1 comment
Labels: bug

#88 - [BUG] Error in run_ancom function due to missing colnames in tax_table of phyloseq object from VIRGO dataset

Issue - State: closed - Opened by xec-cm over 1 year ago
Labels: bug

#87 - [BUG] dplyr::across() warning

Issue - State: closed - Opened by xec-cm over 1 year ago
Labels: bug

#86 - Dev

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

#85 - [BUG] Warning about missing \value sections in man pages

Issue - State: closed - Opened by xec-cm over 1 year ago
Labels: bug

#84 - [BUG] Removal of "pseudo" and "pseudo_sens" Parameters in ANCOMBC Package of Bioconductor's Devel Version

Issue - State: closed - Opened by xec-cm over 1 year ago
Labels: bug

#83 - closes #81

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

#82 - [Feature Request] Update packages to their latest version and ensure smooth functioning

Issue - State: closed - Opened by xec-cm over 1 year ago
Labels: enhancement

#81 - [Feature Request] Update R-cmd-check GitHub Action to Support Latest R and Bioconductor Versions

Issue - State: closed - Opened by xec-cm over 1 year ago
Labels: enhancement

#80 - Dev

Pull Request - State: closed - Opened by xec-cm almost 2 years ago - 3 comments

#79 - [Feature Request] Add size and alpha dimensions in the `mutual_plt()`

Issue - State: closed - Opened by xec-cm almost 2 years ago
Labels: enhancement

#78 - count transformations for plotting (#77 )

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

#77 - [Feature Request] Implement count transfromations for plotting abundances

Issue - State: closed - Opened by xec-cm almost 2 years ago
Labels: enhancement

#76 - Dev

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

#75 - dessert names: remove special characters

Issue - State: closed - Opened by xec-cm almost 2 years ago

#74 - CI/CD errors

Issue - State: closed - Opened by xec-cm almost 2 years ago

#73 - update

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

#72 - Dev

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

#71 - effect direction discrepances only in LEFSE. Why?

Issue - State: closed - Opened by xec-cm almost 2 years ago
Labels: question

#70 - Phy QC

Issue - State: closed - Opened by xec-cm almost 2 years ago

#69 - Migrate to R 4.2 & Bioc 3.16

Issue - State: closed - Opened by xec-cm about 2 years ago

#68 - closes #67

Pull Request - State: closed - Opened by xec-cm about 2 years ago

#67 - github actions update

Issue - State: closed - Opened by xec-cm about 2 years ago
Labels: enhancement

#66 - implementation of var adjustment during modeling

Issue - State: closed - Opened by xec-cm about 2 years ago
Labels: enhancement

#65 - Mutual finding plot for exploratory visualitzation

Issue - State: closed - Opened by xec-cm about 2 years ago
Labels: enhancement

#64 - Plot OTU abundance plots

Issue - State: closed - Opened by xec-cm about 2 years ago
Labels: enhancement

#63 - Phyloseq normalization methods

Issue - State: closed - Opened by xec-cm about 2 years ago
Labels: enhancement

#62 - Dev

Pull Request - State: closed - Opened by xec-cm about 2 years ago

#61 - Revert detectionsparation verson check

Issue - State: closed - Opened by xec-cm about 2 years ago
Labels: enhancement

#60 - No filter the results.

Issue - State: closed - Opened by xec-cm about 2 years ago
Labels: enhancement

#59 - Dev

Pull Request - State: closed - Opened by xec-cm about 2 years ago

#58 - Comparative plot between methods

Issue - State: closed - Opened by xec-cm about 2 years ago
Labels: enhancement, question

#57 - Homogenization of results between methods

Issue - State: closed - Opened by xec-cm about 2 years ago
Labels: bug, enhancement

#56 - Implement `by_comparison` parameter for `step_filter_taxa()` function

Issue - State: closed - Opened by xec-cm about 2 years ago
Labels: enhancement, question

#55 - Capture errors for each method

Issue - State: closed - Opened by xec-cm about 2 years ago
Labels: enhancement

#54 - `step_filter_taxa()` check that some level of the variable of interest is not all 0 after the filter

Issue - State: closed - Opened by xec-cm about 2 years ago
Labels: enhancement

#53 - metagenomeSeq debug contrasts

Issue - State: closed - Opened by xec-cm about 2 years ago
Labels: bug

#52 - correlation heatmap between tested methods

Issue - State: closed - Opened by xec-cm about 2 years ago
Labels: enhancement

#51 - closes #50

Pull Request - State: closed - Opened by xec-cm about 2 years ago

#50 - increase code coverage up to 90%

Issue - State: closed - Opened by xec-cm about 2 years ago
Labels: documentation, enhancement

#49 - Dev

Pull Request - State: closed - Opened by xec-cm about 2 years ago

#48 - Github action for BiocCheck

Issue - State: closed - Opened by xec-cm about 2 years ago
Labels: enhancement

#47 - trasition from ANCOM to ANCOMBC

Issue - State: closed - Opened by xec-cm over 2 years ago
Labels: bug, enhancement

#46 - Update DESCRIPTION

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

#45 - Update pkg_check.R

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

#44 - Dev

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

#43 - `add_var` and `add_tax` methods

Issue - State: closed - Opened by xec-cm over 2 years ago
Labels: enhancement

#42 - subset_samples function

Issue - State: closed - Opened by xec-cm over 2 years ago
Labels: enhancement

#41 - closes #40

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

#40 - package icon and favicons

Issue - State: closed - Opened by xec-cm over 2 years ago
Labels: documentation, enhancement, website

#39 - closes #37

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

#38 - closes #33, closes #34

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

#37 - group function reference

Issue - State: closed - Opened by xec-cm over 2 years ago
Labels: enhancement, website, doc

#36 - viggnet about import/export parametres in json format

Issue - State: closed - Opened by xec-cm over 2 years ago - 1 comment
Labels: enhancement, website, doc

#35 - vignette about how to import data from different formats

Issue - State: closed - Opened by xec-cm over 2 years ago
Labels: enhancement, website, doc

#34 - Update README.Rmd

Issue - State: closed - Opened by xec-cm over 2 years ago
Labels: enhancement, website, doc

#33 - intro / Get Started

Issue - State: closed - Opened by xec-cm over 2 years ago
Labels: enhancement, website, doc

#32 - Dev

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

#31 - Create package web site with pkgdown

Issue - State: closed - Opened by xec-cm over 2 years ago
Labels: enhancement

#30 - SummarizedExperiment2phyloseq

Issue - State: closed - Opened by xec-cm over 2 years ago
Labels: enhancement

#29 - Dev

Pull Request - State: closed - Opened by xec-cm over 2 years ago
Labels: enhancement

#28 - random id with random dessert name

Issue - State: closed - Opened by xec-cm over 2 years ago

#27 - Dev

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

#26 - Log2FC parameter as inactive parametre by defauls

Issue - State: closed - Opened by xec-cm over 2 years ago
Labels: enhancement

#25 - closes #18

Pull Request - State: closed - Opened by xec-cm over 2 years ago
Labels: enhancement

#24 - arrange output of `find_intersections()` by sum_methods

Issue - State: closed - Opened by xec-cm over 2 years ago
Labels: enhancement

#23 - bake method that implements weighting for each of the steps

Issue - State: closed - Opened by xec-cm over 2 years ago - 1 comment
Labels: enhancement

#22 - replace overlap pct to overlap count in bake function

Issue - State: closed - Opened by xec-cm over 2 years ago
Labels: enhancement

#21 - save bake parameters in the json

Issue - State: closed - Opened by xec-cm over 2 years ago
Labels: enhancement

#20 - Exclusion plot

Issue - State: closed - Opened by xec-cm over 2 years ago
Labels: enhancement

#19 - Diff printing for steps that modify the phy object

Issue - State: closed - Opened by xec-cm over 2 years ago
Labels: enhancement

#18 - Implement Wilcox method

Issue - State: closed - Opened by xec-cm over 2 years ago
Labels: enhancement

#17 - implement phyloseq::rarefy_even_depth() as a step

Issue - State: closed - Opened by xec-cm over 2 years ago
Labels: enhancement

#16 - Replace step_ prefixt to dar_

Issue - State: closed - Opened by xec-cm over 2 years ago
Labels: enhancement

#15 - Check if all methods have the default values from the original package

Issue - State: closed - Opened by xec-cm over 2 years ago
Labels: enhancement

#14 - filter phyloseq

Issue - State: closed - Opened by xec-cm over 2 years ago

#13 - metagenomeSeq implementation

Issue - State: closed - Opened by xec-cm over 2 years ago
Labels: enhancement

#12 - DESeq2 implementation

Issue - State: closed - Opened by xec-cm over 2 years ago
Labels: enhancement

#11 - corncob implementation

Issue - State: closed - Opened by xec-cm over 2 years ago
Labels: enhancement

#10 - aldex implementation

Issue - State: closed - Opened by xec-cm over 2 years ago
Labels: enhancement

#9 - ancom implementation

Issue - State: closed - Opened by xec-cm over 2 years ago
Labels: enhancement

#8 - Implement S4 object

Issue - State: closed - Opened by xec-cm over 2 years ago
Labels: enhancement

#7 - error with system.file()

Issue - State: closed - Opened by xec-cm over 2 years ago
Labels: bug

#6 - error r-cmd-check

Issue - State: closed - Opened by xec-cm over 2 years ago
Labels: bug

#5 - Loading functionality

Issue - State: closed - Opened by xec-cm over 2 years ago

#4 - Add internal data

Issue - State: closed - Opened by xec-cm over 2 years ago
Labels: enhancement

#3 - github action check error

Issue - State: closed - Opened by xec-cm over 2 years ago - 1 comment
Labels: bug

#2 - Add github testing

Issue - State: closed - Opened by xec-cm over 2 years ago
Labels: enhancement

#1 - init repo

Issue - State: closed - Opened by xec-cm over 2 years ago
Labels: enhancement

GitHub / microbialgenomics-irsicaixaorg/dar issues and pull requests