ChiLiubio/microeco issues and pull requests

#429 - Plotting actual read counts in Microeco-Class object using original OTU data

Issue - State: open - Opened by JayalalKJ about 1 month ago - 1 comment
Labels: documentation, good first issue

#428 - Help needed: Removing cross-contaminated genera from microtable-class Object

Issue - State: open - Opened by JayalalKJ about 1 month ago - 1 comment
Labels: documentation

#427 - How to import external correlation matrix into res_cor_p?

Issue - State: closed - Opened by Liuyuxinn about 2 months ago - 2 comments
Labels: documentation

#426 - Polite enquiry about "trans_network class"

Issue - State: closed - Opened by PeterPan0106 about 2 months ago - 2 comments
Labels: documentation

#425 - trans_env$cal_autocor p values

Issue - State: open - Opened by alberjo296 about 2 months ago - 2 comments
Labels: documentation

#424 - Issue with order_x

Issue - State: closed - Opened by susheelbhanu about 2 months ago - 2 comments
Labels: documentation

#423 - Error in `[.data.frame`(rres, , rownames(abund_table_sub_lda), drop = FALSE)

Issue - State: open - Opened by shuchong200 about 2 months ago - 2 comments

#422 - FAPROTAX 1.2.10 is available, polite request of update in the package

Issue - State: closed - Opened by PeterPan0106 about 2 months ago - 5 comments
Labels: enhancement

#421 - Filtering ASVs/OTUs based on FungalTraits

Issue - State: open - Opened by alejorojas2 about 2 months ago - 1 comment

#418 - Errors using newly generated microtable from phyloseq components

Issue - State: open - Opened by AngelicaMiraples about 2 months ago - 2 comments
Labels: documentation

#417 - Question about plot_scatterfit

Issue - State: open - Opened by meredithds about 2 months ago - 3 comments
Labels: documentation

#416 - Modifying colors to cal_autcor

Issue - State: open - Opened by Manso002 about 2 months ago - 1 comment
Labels: documentation

#415 - LEFSE result inconsistent with taxa distribution among groups

Issue - State: open - Opened by jamorillo 2 months ago - 4 comments
Labels: documentation

#414 - Error in lefse$res_diff is NULL

Issue - State: closed - Opened by JamShaw229 2 months ago

#413 - doubts about taxonomy heatmap

Issue - State: open - Opened by jamorillo 2 months ago - 2 comments
Labels: good first issue

#412 - trans_diff$new with method "DESeq2" causes error.

Issue - State: open - Opened by 145218415 2 months ago - 5 comments
Labels: documentation, enhancement, good first issue

#411 - lefse analysis questions and plotting without tags

Issue - State: open - Opened by Roctry 3 months ago - 3 comments

#410 - when run trans_alpha$new, Skip 'Chao1', 'ACE' and 'Observed' ...

Issue - State: closed - Opened by wanjinhu 3 months ago - 2 comments

#409 - Inconsistent results from workflow in tutorial 4.2 trans_venn class

Issue - State: closed - Opened by jarrodscott 3 months ago - 3 comments
Labels: enhancement

#408 - Error in `[.data.frame`(rres, , rownames(abund_table_sub_lda), drop = FALSE)

Issue - State: closed - Opened by hlwCoBi 3 months ago - 4 comments
Labels: documentation

#407 - Get -Inf LDA value when use lefse analysis

Issue - State: closed - Opened by monaye745 3 months ago - 5 comments
Labels: documentation

#406 - chorddiagram : cal_sum_links

Issue - State: closed - Opened by Ananya1006 3 months ago - 9 comments
Labels: enhancement

#405 - chorddiagram : cal_sum_links

Issue - State: closed - Opened by Ananya1006 3 months ago
Labels: duplicate

#404 - How to extract a subset based on the name of a node using subset_network？

Issue - State: closed - Opened by Liuyuxinn 3 months ago - 8 comments
Labels: documentation

#403 - How can I do venn/β-diversity analysis at higher taxonomic level

Issue - State: open - Opened by jieyin2023 3 months ago - 1 comment
Labels: documentation

#402 - Is it possible to use microeco to screen for 'rare/abundant taxa'?

Issue - State: closed - Opened by makerer5 3 months ago - 3 comments
Labels: documentation

#401 - Some questions about trans_network class

Issue - State: closed - Opened by Liuyuxinn 3 months ago - 5 comments
Labels: documentation

#399 - LEfSe - subgroup check did not remove non-significant taxa

Issue - State: closed - Opened by NNTLe 3 months ago - 8 comments
Labels: documentation

#398 - Problem with representation of dbRDA

Issue - State: open - Opened by alberjo296 3 months ago - 15 comments
Labels: documentation

#397 - get_node_table failed to calculate node roles for all taxa

Issue - State: closed - Opened by scilexenko 4 months ago - 3 comments
Labels: documentation

#396 - SpiecEasi::spiec.easi in cal_network doesn't seem to change a thing

Issue - State: closed - Opened by scilexenko 4 months ago - 2 comments

#395 - get correlation matrix from trans_network$new

Issue - State: closed - Opened by scilexenko 4 months ago - 2 comments
Labels: documentation

#394 - Error in rbind(deparse.level, ...) : numbers of columns of arguments do not match

Issue - State: closed - Opened by wskaerc 4 months ago - 2 comments
Labels: bug

#393 - Mantel test and Pearson's correlation

Issue - State: open - Opened by johagcoria 4 months ago - 1 comment
Labels: documentation

#392 - Error in cal_spec_func(fungi_database="FUNGuid"

Issue - State: open - Opened by AlbertoBernacchi 4 months ago - 1 comment

#391 - Trans Gamma diversity, sample dots not seen within the confidence interval

Issue - State: closed - Opened by CYBERBOY1210 4 months ago - 2 comments
Labels: enhancement

#390 - Clarity on the "use_group_list = TRUE" in trans_func functions

Issue - State: open - Opened by biazen123 4 months ago - 1 comment

#389 - NA in Relative abundance graph

Issue - State: open - Opened by AnnaMarizzi 4 months ago - 3 comments
Labels: documentation

#388 - humann2meco -Some (unclassified) entries in the meco OTU table are assigned with negative entries

Issue - State: closed - Opened by barnali-waugh 4 months ago - 3 comments
Labels: documentation

#387 - LEfSe's results look different than before

Issue - State: open - Opened by wfgui 4 months ago - 9 comments
Labels: enhancement, good first issue

#386 - How do CCA calculations use the first 10 Phylum/Genus?

Issue - State: closed - Opened by makerer5 5 months ago - 3 comments
Labels: documentation

#385 - The plot generated by the 'plot_diff_cladogram' function appears unusual and difficult to interpret.

Issue - State: open - Opened by lzuChengweiZhang 5 months ago - 3 comments
Labels: documentation, good first issue

#383 - Error while differential analysis with aldex2 with humann stratified files

Issue - State: open - Opened by RoyDibakar 5 months ago - 14 comments
Labels: documentation

#382 - Error in lefse$plot_diff_cladogram

Issue - State: closed - Opened by YP-Hao 5 months ago - 3 comments
Labels: duplicate

#380 - Plot_diff_abund improvement

Issue - State: closed - Opened by DpennaS 5 months ago - 1 comment
Labels: enhancement

#379 - Query Regarding Paired Sample Analysis with `trans_diff` Function

Issue - State: open - Opened by learn-lx-zhu 5 months ago - 3 comments
Labels: documentation

#377 - Error in trans_diff$new by method = "lefse"

Issue - State: closed - Opened by cheng-xd 5 months ago - 8 comments
Labels: documentation, duplicate

#376 - Plotting Relative Abundance Graph with 3 Factors

Issue - State: open - Opened by amandamanully 5 months ago - 1 comment

#375 - Error while importing HUMAnN unstratified table

Issue - State: open - Opened by anw-sh 5 months ago - 6 comments
Labels: documentation, good first issue

#374 - Taxa labels dont show up in plot_diff_cladogram

Issue - State: closed - Opened by jackqio 6 months ago - 2 comments
Labels: documentation

#373 - Adding exting network

Issue - State: closed - Opened by DpennaS 6 months ago - 9 comments
Labels: good first issue

#372 - Correlation of an ASV with various environmental variables

Issue - State: open - Opened by guianrey 6 months ago - 1 comment
Labels: documentation

#371 - ggcor needed for Mantel test + Correlation heatmap is no longer available

Issue - State: closed - Opened by eperezv 6 months ago - 2 comments
Labels: documentation

#369 - merge function doubt

Issue - State: open - Opened by jamorillo 6 months ago - 2 comments
Labels: documentation

#368 - Error when running cal_mantel_corr

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

#367 - Taxa labels dont show up after performing plot_diff_cladogram

Issue - State: closed - Opened by BiggusDickus666 6 months ago - 8 comments
Labels: documentation, good first issue

#366 - Error in dataset$tidy_dataset()

Issue - State: closed - Opened by Ye-Yonglian 6 months ago - 2 comments
Labels: duplicate

#364 - Error in private$tidy_samples(self)

Issue - State: closed - Opened by fafuwjw 6 months ago - 9 comments
Labels: enhancement

#362 - What does the se.ACE in the microbial alpha diversity index indicate

Issue - State: closed - Opened by makerer5 7 months ago - 1 comment
Labels: documentation

#361 - Error in x[[p]] : subscript out of bounds

Issue - State: open - Opened by yumiao222222 7 months ago - 3 comments
Labels: documentation

#360 - dbRDA results

Issue - State: closed - Opened by DimitraIoli 7 months ago - 2 comments
Labels: documentation

#359 - Cal_alphadiv skips observed

Issue - State: closed - Opened by Manso002 7 months ago - 3 comments
Labels: documentation

#358 - cal_cor() correlation between diversity metrics and env factors?

Issue - State: closed - Opened by marwa38 7 months ago - 4 comments
Labels: documentation

#357 - problem with downloading abundance table

Issue - State: closed - Opened by guianrey 7 months ago - 2 comments
Labels: documentation

#356 - assign named colors to 'plot_sum_links'

Issue - State: closed - Opened by chrissy005 7 months ago - 2 comments
Labels: documentation

#355 - Sample ID in rarefactions curves

Issue - State: closed - Opened by jamorillo 7 months ago - 2 comments
Labels: enhancement

#354 - tidy_taxonomy function do not properly perform tax_table clean up

Issue - State: open - Opened by BiggusDickus666 7 months ago - 4 comments
Labels: documentation, good first issue

#353 - Taxa assigned incorrectly to different groups in trans_func plots

Issue - State: open - Opened by MarwaElnaiem 7 months ago - 1 comment

#352 - Error in method = cicrlize with plot_sum_links

Issue - State: closed - Opened by chrissy005 8 months ago - 8 comments

#351 - can you add method =" euclidean” of microtable$cal_betadiv?

Issue - State: closed - Opened by milyzhou 8 months ago - 1 comment
Labels: documentation

#350 - unused argument error

Issue - State: open - Opened by tenguzame 8 months ago - 1 comment
Labels: documentation

#349 - Chao1 index is the same with observed.

Issue - State: closed - Opened by WangWaud 8 months ago - 4 comments

#348 - Can't find function trans_ordination

Issue - State: closed - Opened by Jgruetzke 8 months ago - 3 comments

#347 - Does cal_network() use relative abundance to make a network?

Issue - State: closed - Opened by WangWaud 8 months ago - 1 comment
Labels: documentation

#346 - FAPROTAX update

Issue - State: closed - Opened by jackqio 8 months ago - 1 comment
Labels: enhancement

#345 - R Session Aborted R encountered a fatal error The session was terminated

Issue - State: open - Opened by makerer5 8 months ago - 4 comments
Labels: documentation

#344 - How to re order sample ID in a barplot

Issue - State: closed - Opened by srisvs33 8 months ago - 2 comments
Labels: documentation

#343 - MEGAN output to microeco

Issue - State: open - Opened by spe238 8 months ago - 1 comment

#342 - Error in reproducing the relative abundance figure

Issue - State: closed - Opened by srisvs33 8 months ago - 2 comments

#341 - taxa nested bug?

Issue - State: closed - Opened by jamorillo 8 months ago - 12 comments
Labels: documentation, good first issue

#340 - t1$cal_group_distance_diff with two variables

Issue - State: closed - Opened by milyzhou 9 months ago - 5 comments
Labels: enhancement

#339 - trans_diff$new with two variables

Issue - State: closed - Opened by milyzhou 9 months ago - 3 comments
Labels: enhancement

#338 - Error in rep(1, nrow(edges)) When running plot_diff_cladogram

Issue - State: closed - Opened by Harr7y 9 months ago - 8 comments
Labels: documentation

#337 - how to select a group as reference per run MaAsLin2 diferential abundance analysis

Issue - State: open - Opened by milyzhou 9 months ago - 1 comment
Labels: documentation

#336 - How to extract the contribution of a variable to the principal component (percentage)

Issue - State: open - Opened by milyzhou 9 months ago - 1 comment
Labels: documentation

#335 - t1 <- trans_diff$new(dataset = dataset, method = "metagenomeSeq", group = "Group", taxa_level = "Genus") #Error in h(simpleError(msg, call)) : Error in evaluating 'x' argument for selecting a method for the 'unique' function: There is no function called "setkey".

Issue - State: closed - Opened by xinguo1236 9 months ago - 5 comments
Labels: documentation

#334 - t1 <- trans_diff$new(dataset = dataset, method = "metagenomeSeq", group = "Group", taxa_level = "Genus") #Error in h(simpleError(msg, call)) : Error in evaluating 'x' argument for selecting a method for the 'unique' function: There is no function called "setkey".

Issue - State: closed - Opened by xinguo1236 9 months ago

#333 - d1 <- dataset$merge_taxa(taxa = "Genus") Error in check_tax_level(taxa, self) : 没有"check_tax_level"这个函数

Issue - State: closed - Opened by xinguo1236 9 months ago - 9 comments

#331 - Error in guides_train(scales = scales$non_position_scales(), theme = theme, : could not find function "guides_train"

Issue - State: closed - Opened by PPpissar 9 months ago - 4 comments
Labels: documentation

GitHub / ChiLiubio/microeco issues and pull requests