YuLab-SMU/MicrobiotaProcess issues and pull requests

#124 - alpha index statistics

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

#123 - Issue in ggdiffclade

Issue - State: open - Opened by scoob24 3 months ago - 1 comment

#122 - rarefy Abundance and rare abundance

Issue - State: open - Opened by Muneer111 6 months ago

#121 - Exporting MPSE generated variables

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

#120 - Using mp_diff_analysis for FAPROTAX functional data and visualization

Issue - State: open - Opened by MizaR108 6 months ago

#119 - Redundant labels in taxonomic name

Issue - State: closed - Opened by MizaR108 6 months ago - 2 comments

#118 - 如何通过物种丰度矩阵，物种分类表，样本分组信息构建MPSE对象

Issue - State: open - Opened by zyc134 7 months ago

#117 - ggrarecurve报错Error in if (obj %>% rowSums %>% var != 0 && !force)

Issue - State: open - Opened by Elixir0822 7 months ago

#116 - 示例运行报错。

Issue - State: closed - Opened by liuninghua521 7 months ago - 1 comment

#115 - Report: Large memory usage when run `mp_cal_abundance`

Issue - State: open - Opened by alienzj 8 months ago - 1 comment

#114 - update CITATION

Pull Request - State: closed - Opened by Clearmind777 10 months ago

#113 - Possible to calculate diff_analysis with less than 5 sample per group ?

Issue - State: open - Opened by UpalabdhaD 11 months ago - 2 comments

#112 - how can I change the fact_label order in mp_plot_abundance?

Issue - State: closed - Opened by 1870694249 11 months ago - 1 comment

#111 - add labels to plot from ggrarecurve

Issue - State: open - Opened by soluna1 11 months ago

#110 - diff_analysis with multiple groups

Issue - State: open - Opened by dalferes 11 months ago

#109 - diff_analysis without rarefying

Issue - State: open - Opened by cmetadea 11 months ago

#108 - diff_analysis in ver 1.14.0

Issue - State: open - Opened by RIJP-SU 11 months ago

#107 - Confidance interval returns NA values

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

#106 - mp_diff_analysis with CoDA algorithms

Issue - State: open - Opened by MEladawi almost 1 year ago

#105 - 导入qiime2输出内存不足

Issue - State: closed - Opened by yjiakang about 1 year ago - 2 comments

#104 - parsing the output of qiime2出错

Issue - State: closed - Opened by benzodiazepines about 1 year ago - 1 comment

#103 - qiime2 alpha稀释曲线readsNums异常

Issue - State: closed - Opened by yjiakang about 1 year ago - 1 comment

#102 - Error occurred while parsing the output of qiime2

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

#101 - How to add the p value to the marginal box-andwhisker of the PCo plot

Issue - State: open - Opened by J5886 about 1 year ago

#100 - Include the percentage values in the stacked plots

Issue - State: open - Opened by antoniobio about 1 year ago - 5 comments

#99 - rmun NOT work by default

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

#98 - updated mp_import_humann_regroup to keep the abundance of contributed taxa

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

#97 - Two question about import qiime2 files

Issue - State: open - Opened by Rainjie-afk over 1 year ago - 2 comments

#96 - The normalisation in getpcoa() function does not work

Issue - State: open - Opened by fernando-aq over 1 year ago - 2 comments

#95 - 关于mp_import_metaphlan中输入treefile错误的问题

Issue - State: open - Opened by Brynnhildr over 1 year ago - 2 comments

#94 - 如何调整Biomarker可视化过程中，显示label的数量

Issue - State: open - Opened by liuninghua521 over 1 year ago - 3 comments

#93 - test_differential_abundance with batch effect

Issue - State: open - Opened by MEladawi over 1 year ago - 3 comments

#92 - mp_cal_venn and mp_plot_venn calculation

Issue - State: closed - Opened by etorres475 over 1 year ago - 2 comments

#91 - Summarizing data from mpse object without changing class

Issue - State: closed - Opened by etorres475 over 1 year ago - 9 comments

#90 - About mp_rrarefy and mp_cal_rarecurve

Issue - State: open - Opened by lbwfff over 1 year ago - 4 comments

#89 - Wrong: no applicable method for 'unnest' applied to an object of class

Issue - State: open - Opened by Wengen-Zhu over 1 year ago - 2 comments

#88 - Error of mp_import_metaphlan

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

#87 - Biomarker discovery: Error in if (nrow(tmpkeepfeature) > 0) { : argument is of length zero

Issue - State: closed - Opened by etorres475 over 1 year ago - 7 comments

#86 - include.lowest = FALSE in mp_filter_taxa seems not work

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

#85 - Rarecurve output range

Issue - State: open - Opened by IS233489 over 1 year ago - 3 comments

#84 - No method defined for class MPSE.

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

#83 - Problem with the ggtree and ggtree extra

Issue - State: open - Opened by gregnoel over 1 year ago - 5 comments

#82 - mp_plot_diff_manhattan mp_plot_diff_cladogram set_diff_boxplot_color

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

#81 - !!!!! ggdiffclade issue

Issue - State: open - Opened by LeeJH5120 over 1 year ago - 3 comments

#80 - mp_plot_diff_manhattan error

Issue - State: closed - Opened by shashank-KU over 1 year ago - 8 comments

#79 - ggbox - testmethod and p-value correction

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

#78 - PCoA ordination of beta diversity along with genera and other environmental factors?

Issue - State: open - Opened by marwa38 almost 2 years ago - 3 comments

#77 - mp_extract_abundance() errors?

Issue - State: open - Opened by marwa38 almost 2 years ago - 4 comments

#76 - rarefaction for first quartile?

Issue - State: open - Opened by marwa38 almost 2 years ago - 5 comments

#75 - Is there any easy way to assign a universal color pattern for taxa between different MPSEs?

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

#74 - biomarker discovery

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

#73 - get_pca(): extract PC1:PC3 % variation explained (values)

Issue - State: closed - Opened by MaryoHg about 2 years ago - 2 comments

#72 - How to rearrange samples on barplot based on abundance?

Issue - State: open - Opened by Jawen-D about 2 years ago - 2 comments

#71 - Filtering data

Issue - State: open - Opened by DanielSoutoV about 2 years ago - 2 comments

#70 - set_diff_boxplot_color not found

Issue - State: closed - Opened by olivierrue about 2 years ago - 2 comments

#69 - could not find function "stop_wrap"

Issue - State: open - Opened by nbutyrate about 2 years ago - 2 comments

#68 - Error in if (nrow(tmpkeepfeature) > 0) { : argument is of length zero

Issue - State: open - Opened by freixas84 about 2 years ago - 1 comment

#67 - updated online vignette URL

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

#66 - Weird Rarecurve

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

#65 - fc.method = "compare_mean" can run but fc.method = "compare_median" can't run

Issue - State: open - Opened by shaodongyan over 2 years ago - 7 comments

#64 - Get_NRI_NTI function

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

#63 - The Function "browseVignettes("MicrobiotaProcess")" have not work

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

#62 - How to solve this error?

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

#61 - mp_plot_abundance()功能X轴样本排序

Issue - State: open - Opened by liuninghua521 over 2 years ago - 2 comments

#60 - How to make MPSE object?

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

#59 - How to get a Y-axis with distance scale with ggclust(layout = "dendrogram") and sample names at tips

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

#58 - How to import the output file from MetaPhlan?

Issue - State: closed - Opened by paiboon-aut over 2 years ago - 2 comments

#57 - how to get P value in get_pcoa?

Issue - State: open - Opened by Feeling-ll over 2 years ago - 2 comments

#56 - lapply() to loop over mp_plot_rarecurve()

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

#55 - How to use ggbox() with data.frame?

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

#54 - update Introduction.Rmd

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

#53 - Questions about `mp_import_dada2` and `mp_cal_rarecurve` function

Issue - State: open - Opened by alienzj over 2 years ago - 6 comments

#52 - Diff analysis at specific taxonomic level and FDR

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

#51 - 将phyloseq转换为mp遇到问题

Issue - State: open - Opened by liuninghua521 over 2 years ago - 2 comments

#50 - mp_plot_abundance函数调整X轴样本顺序

Issue - State: open - Opened by liuninghua521 over 2 years ago - 3 comments

#49 - mp_plot_abundance dose not generate a plot

Issue - State: closed - Opened by akhst7 over 2 years ago - 1 comment

#48 - MicrobiotaProcess.rdb' is corrupt

Issue - State: closed - Opened by akhst7 over 2 years ago

#47 - Install problems!!!

Issue - State: open - Opened by vee3capp over 2 years ago - 4 comments

#46 - could not find function "mp_plot_diff_res"

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

#45 - biomarker discovery

Issue - State: open - Opened by MonaLiu421 over 2 years ago - 1 comment

#44 - How to label Taxanomy information in the taxa tree

Issue - State: open - Opened by taekwonleo-yuhao over 2 years ago - 8 comments

#43 - ggdiffbox

Issue - State: open - Opened by MonaLiu421 over 2 years ago - 10 comments

#42 - Abundance visualization for specific taxa

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

#41 - mp_plot_abundance geom flowbar modifying width

Issue - State: closed - Opened by remi-leguern almost 3 years ago - 2 comments

#40 - Encounter errors in diff_analysis

Issue - State: closed - Opened by Turbinenoli almost 3 years ago - 6 comments

#39 - the problem ggtree with MPSE object

Issue - State: closed - Opened by padingdun833 almost 3 years ago - 4 comments

#38 - can't calculate metaphlan's output

Issue - State: open - Opened by shaodongyan almost 3 years ago - 6 comments

#37 - phyloseq and ggnewscale is required when install MicrobiotaProcess in Ubuntu

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

#36 - Seems `filter` function from dplyr dose not work for class MPSE for now？

Issue - State: closed - Opened by Hua-CM about 3 years ago - 4 comments

#35 - Biomarker discovery explanation and new package's feature discussion

Issue - State: open - Opened by alienzj about 3 years ago - 36 comments

#34 - How to integrate the class with picrust2?

Issue - State: closed - Opened by dikiprawisuda about 3 years ago - 1 comment

#33 - get_pca error

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

#32 - Installation Error:ERROR: object 'get_aes_var' is not exported by 'namespace:rvcheck'

Issue - State: open - Opened by chywang17 about 3 years ago - 7 comments

#31 - Related project based on TreeSummarizedExperiment

Issue - State: open - Opened by antagomir about 3 years ago - 2 comments

#30 - How to convert phloseq object to MPSE object properly with funtion as.MPSE

Issue - State: open - Opened by taekwonleo-yuhao about 3 years ago - 7 comments

GitHub / YuLab-SMU/MicrobiotaProcess issues and pull requests