MicrobialGenomics-IrsicaixaOrg/dar

Issues

• [BUG] Temporary Suspension of corncob Functionality

  #110 opened 9 months ago by xec-cm
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• [BIOCONDUCOR REVIEW / R] Consider using a more descriptive class name for recipe.

  #104 opened 10 months ago by xec-cm
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• [BIOCONDUCTOR REVIEW / R] Generally, methods and generics are not needed if they are defined for a single class.

  #105 opened 10 months ago by xec-cm
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• [BIOCONDUCTOR REVEIW / R] Please consider using `SummarizedExperiment`'s method for `subset`ting.

  #109 opened 10 months ago by xec-cm
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• [BIOCONDUCTOR REVIEW] Accept TSE as input of recipe

  #108 opened 10 months ago by xec-cm
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• [BIOCONDUCOR REVIEW / R] Avoid setting a seed within a function `run_aldex`

  #103 opened 10 months ago by xec-cm
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• [BIOCONDUCTOR REVIEW / R] Avoid recommending unconventional package installation methods, e.g., `pak::pkg_install`

  #102 opened 10 months ago by xec-cm
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• [BIOCONDUCTOR REVIEW] / Avoid re-exporting functions such as `%>%` and `:=`

  #101 opened 10 months ago by xec-cm
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• [BIOCONDUCTOR REVIEW / R] use the data name in the documentation `R/data.R` rather than `NA`.

  #106 opened 10 months ago by xec-cm
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• [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).

  #99 opened 10 months ago by xec-cm
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• [BIOCONDUCOR REVIEW / NAMWSPACE] `required_deps` seems to be an internal function and does not need to be exported.

  #100 opened 10 months ago by xec-cm
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• [BIOCONDUCTOR REVIEW / DESCRIPTION] R version dependency should be 4.4.0 or higher

  #98 opened 10 months ago by xec-cm
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• [BUG] Update github action to new Bioconducotor 3.19

  #107 opened a year ago by xec-cm
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• [BUG] R CMD CHECK Warining on linux

  #97 opened a year ago by xec-cm
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• [BUG] R CMD BUILD warning

  #96 opened a year ago by xec-cm
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• [BUG] testhat read_data error with setequal

  #95 opened a year ago by xec-cm
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• [Feature Request] Try to extract stats with workflow-telemetry-action

  #93 opened a year ago by xec-cm
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• [BUG] codecov badge from main to devel

  #91 opened a year ago by xec-cm
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• [BUG] Convergence Issue in `corncob` when using `corncob::differentialTest()`

  #89 opened a year ago by xec-cm
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• [BUG] Error in run_ancom function due to missing colnames in tax_table of phyloseq object from VIRGO dataset

  #88 opened a year ago by xec-cm
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• [BUG] dplyr::across() warning

  #87 opened a year ago by xec-cm
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• [BUG] Warning about missing \value sections in man pages

  #85 opened a year ago by xec-cm
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• [Feature Request] Update R-cmd-check GitHub Action to Support Latest R and Bioconductor Versions

  #81 opened a year ago by xec-cm
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• [BUG] Removal of "pseudo" and "pseudo_sens" Parameters in ANCOMBC Package of Bioconductor's Devel Version

  #84 opened a year ago by xec-cm
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• [Feature Request] Update packages to their latest version and ensure smooth functioning

  #82 opened a year ago by xec-cm
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• [Feature Request] Add size and alpha dimensions in the `mutual_plt()`

  #79 opened a year ago by xec-cm
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• [Feature Request] Implement count transfromations for plotting abundances

  #77 opened 2 years ago by xec-cm
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• effect direction discrepances only in LEFSE. Why?

  #71 opened 2 years ago by xec-cm
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• implementation of var adjustment during modeling

  #66 opened 2 years ago by xec-cm
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• Capture errors for each method

  #55 opened 2 years ago by xec-cm
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• Implement `by_comparison` parameter for `step_filter_taxa()` function

  #56 opened 2 years ago by xec-cm
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• Comparative plot between methods

  #58 opened 2 years ago by xec-cm
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• Phyloseq normalization methods

  #63 opened 2 years ago by xec-cm
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• CI/CD errors

  #74 opened 2 years ago by xec-cm
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• dessert names: remove special characters

  #75 opened 2 years ago by xec-cm
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• Plot OTU abundance plots

  #64 opened 2 years ago by xec-cm
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• Mutual finding plot for exploratory visualitzation

  #65 opened 2 years ago by xec-cm
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• Phy QC

  #70 opened 2 years ago by xec-cm
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• github actions update

  #67 opened 2 years ago by xec-cm
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• Migrate to R 4.2 & Bioc 3.16

  #69 opened 2 years ago by xec-cm
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• No filter the results.

  #60 opened 2 years ago by xec-cm
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• Revert detectionsparation verson check

  #61 opened 2 years ago by xec-cm
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• Homogenization of results between methods

  #57 opened 2 years ago by xec-cm
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• correlation heatmap between tested methods

  #52 opened 2 years ago by xec-cm
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• metagenomeSeq debug contrasts

  #53 opened 2 years ago by xec-cm
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• `step_filter_taxa()` check that some level of the variable of interest is not all 0 after the filter

  #54 opened 2 years ago by xec-cm
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• increase code coverage up to 90%

  #50 opened 2 years ago by xec-cm
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• Github action for BiocCheck

  #48 opened 2 years ago by xec-cm
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• trasition from ANCOM to ANCOMBC

  #47 opened 2 years ago by xec-cm
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• `add_var` and `add_tax` methods

  #43 opened 2 years ago by xec-cm
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