Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / ChiLiubio/microeco issues and pull requests

#319 - missing value where TRUE/FALSE needed with cal_diff(method = "anova")

Issue - State: closed - Opened by MarwaElnaiem 10 months ago - 2 comments
Labels: documentation

#318 - Change text type and colors of taxa names in plot_heatmap

Issue - State: open - Opened by Taiyou187 10 months ago - 3 comments
Labels: documentation

#316 - Taxonomic names in LeFSe plot

Issue - State: closed - Opened by DpennaS 10 months ago - 2 comments
Labels: documentation

#315 - PerMANOVA for trans_alpha$cal_diff()

Issue - State: closed - Opened by biazen123 10 months ago - 2 comments
Labels: documentation

#314 - Pielou metric for alpha diversity is not working

Issue - State: closed - Opened by Ilaria-Pirona 10 months ago - 1 comment

#309 - significance letter in plot_diff

Issue - State: closed - Opened by DpennaS 10 months ago - 2 comments
Labels: documentation

#308 - Applicability of Residual randomization in permutation procedures (RRPP) in Microeco

Issue - State: open - Opened by biazen123 10 months ago - 1 comment
Labels: good first issue

#307 - Mantel + Correlation heatmap

Issue - State: closed - Opened by DpennaS 10 months ago - 6 comments
Labels: good first issue

#306 - Errors in matching the OTU names in the OTU table and the tree

Issue - State: closed - Opened by haitilin 10 months ago - 2 comments
Labels: documentation

#305 - trans_env class CCA module title error

Issue - State: closed - Opened by makerer5 10 months ago - 2 comments
Labels: bug

#304 - plot_bar yields different scale for relative abundance when using high_level

Issue - State: closed - Opened by lixiaopi1985 11 months ago - 1 comment
Labels: documentation

#303 - Error when run lefse analysis

Issue - State: closed - Opened by LAmethyst 11 months ago - 4 comments

#301 - More than 1 or 2 environmental data in microtable

Issue - State: closed - Opened by biazen123 11 months ago - 7 comments

#300 - Category 'unidentified' when analyzing the relative abundance of species

Issue - State: closed - Opened by bfalco 12 months ago - 7 comments
Labels: enhancement

#299 - NMDS aesthetics

Issue - State: closed - Opened by jamorillo 12 months ago - 2 comments
Labels: enhancement, good first issue

#297 - cal_mantel_corr()

Issue - State: closed - Opened by chrissy005 12 months ago - 3 comments

#296 - Distance attenuation relationship

Issue - State: closed - Opened by makerer5 12 months ago - 3 comments
Labels: documentation

#295 - Distance attenuation relationship

Issue - State: closed - Opened by makerer5 12 months ago

#294 - Calculate the mean relative abundance with two variables

Issue - State: closed - Opened by bfalco 12 months ago - 10 comments
Labels: documentation

#293 - Error: Input colors are not enough to use

Issue - State: closed - Opened by bingheer about 1 year ago - 5 comments

#292 - change color

Issue - State: closed - Opened by jimena18-O about 1 year ago - 3 comments

#291 - ploting specific taxa

Issue - State: open - Opened by jamorillo about 1 year ago - 7 comments
Labels: bug, enhancement

#289 - why some otu were omiited when doing trans_venn ?

Issue - State: closed - Opened by Chuan-Jiang about 1 year ago - 4 comments

#288 - extracting p-values and correlation from cal_spe_func result

Issue - State: closed - Opened by galud27 about 1 year ago - 2 comments
Labels: documentation

#287 - choose own colours for plots

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

#286 - 网络分析中无法成功运行CPU多线程

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

#285 - dbRDA flipping vector directions

Issue - State: closed - Opened by spencerlong1 about 1 year ago - 2 comments
Labels: bug

#284 - Taxonomic rank names

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

#283 - Merge two otu tables

Issue - State: closed - Opened by MiaCoco about 1 year ago - 4 comments

#281 - Convert net_construct or net_analyse object to trans_network or cal_network class

Issue - State: open - Opened by chrissy005 about 1 year ago - 16 comments
Labels: good first issue

#280 - The metagenomics code

Issue - State: closed - Opened by CYBERBOY1210 about 1 year ago - 1 comment

#279 - Can you help me with plot_diff_cladogram?

Issue - State: closed - Opened by CTTST about 1 year ago - 3 comments
Labels: good first issue

#278 - lefse plot

Issue - State: closed - Opened by jimena18-O about 1 year ago - 3 comments

#276 - phyloseq2meco function of microeco doesnt work for me

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

#275 - trans_network

Issue - State: closed - Opened by Hobgoblin8 about 1 year ago - 3 comments
Labels: enhancement

#273 - About trans_diff$plot_diff_abund function: reorder taxa according to P.adj

Issue - State: closed - Opened by kestlermai about 1 year ago - 2 comments
Labels: good first issue

#272 - Cal_cor: Not all variable in the correlation matrix

Issue - State: closed - Opened by RoyDibakar about 1 year ago - 6 comments
Labels: documentation

#271 - cal_cor. Environmental factors and some important taxa

Issue - State: closed - Opened by jimena18-O over 1 year ago - 6 comments

#270 - Change the name of the axes and the name of the variables from English to Spanish in the graphs

Issue - State: closed - Opened by jimena18-O over 1 year ago - 2 comments
Labels: documentation

#269 - doubt trans_beta

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

#268 - font size is small

Issue - State: closed - Opened by mvtejesvi over 1 year ago - 3 comments

#267 - ancombc2 problems with taxa´s ?

Issue - State: closed - Opened by Christian-Benjamin over 1 year ago - 11 comments

#266 - Error running FlashWeave

Issue - State: closed - Opened by eperezv over 1 year ago - 4 comments

#265 - Two questions about RDA analysis

Issue - State: closed - Opened by lizhaojie1025 over 1 year ago - 3 comments

#264 - Error when calculating alpha difference using cal_diff()

Issue - State: closed - Opened by finally-jay over 1 year ago - 4 comments

#263 - questions about db-RDA implementation

Issue - State: open - Opened by jamorillo over 1 year ago - 2 comments
Labels: enhancement

#262 - Network modularity accounting for positive and negative interactions

Issue - State: open - Opened by spencerlong1 over 1 year ago - 6 comments
Labels: documentation

#261 - An Error in trans_env$cal_diff (), method = "KW_dunn"

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

#260 - Plotting the colors with the positive and negative correlations.

Issue - State: closed - Opened by Aristotle1992 over 1 year ago - 4 comments
Labels: documentation

#259 - No valid result obtained for this network

Issue - State: closed - Opened by UhP88 over 1 year ago - 8 comments
Labels: documentation

#258 - Error in plot_diff_cladogram

Issue - State: closed - Opened by StanleyDeng27 over 1 year ago - 5 comments
Labels: bug, enhancement

#257 - Taxa4Fun2: Predicting functions for 18S amplicon data

Issue - State: closed - Opened by rgn06 over 1 year ago - 2 comments

#256 - Error in trans_diff ancombc2

Issue - State: closed - Opened by zhaohanshuang over 1 year ago - 4 comments
Labels: documentation

#254 - Error in plot_diff_cladogram

Issue - State: closed - Opened by diego00012138 over 1 year ago - 4 comments

#253 - Error in KW_dunn (Dunn's Kruskal-Wallis Multiple Comparisons)

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

#252 - trans_diff$new with method "rf" causes error.

Issue - State: closed - Opened by Rob-murphys over 1 year ago - 1 comment

#251 - warning from ggplot, NMDS, shape in ordination.

Issue - State: open - Opened by marwa38 over 1 year ago - 12 comments
Labels: documentation, enhancement

#250 - trans_diff with lefse method returns Negative numbers of LDA

Issue - State: closed - Opened by Irisescat over 1 year ago - 3 comments
Labels: bug

#249 - No sample_table provided,

Issue - State: closed - Opened by Geize over 1 year ago - 6 comments

#248 - grouping in beta diversity (..., group = ,) and manova analysis using call_manova_set()?

Issue - State: closed - Opened by marwa38 over 1 year ago - 7 comments
Labels: documentation

#247 - taxonomic composition by highest abundace?

Issue - State: closed - Opened by marwa38 over 1 year ago - 12 comments
Labels: good first issue

#245 - add taxonomy to ASV-level heatmaps

Issue - State: closed - Opened by jamorillo over 1 year ago - 4 comments
Labels: good first issue

#242 - i meet issue during network analysis

Issue - State: closed - Opened by Seoki0903 over 1 year ago - 1 comment

#241 - trans_norm adding a new method?

Issue - State: closed - Opened by marwa38 over 1 year ago - 12 comments
Labels: enhancement, good first issue

#240 - Venn diagram by area?

Issue - State: open - Opened by marwa38 over 1 year ago - 2 comments
Labels: enhancement

#239 - t2$plot_spe_func_perc(use_group_list = TRUE)

Issue - State: closed - Opened by apoosakkannu over 1 year ago - 1 comment

#238 - Heatmap of single taxa

Issue - State: closed - Opened by hkittner over 1 year ago - 2 comments
Labels: good first issue

#237 - aldex2 effect size calculations

Issue - State: closed - Opened by ShailNair over 1 year ago - 2 comments
Labels: documentation

#236 - threshold shared ASV Venn diagramm

Issue - State: closed - Opened by cdeschamps63 over 1 year ago - 1 comment
Labels: documentation

#235 - maaslin2 as differential abundance method?

Issue - State: closed - Opened by marwa38 over 1 year ago - 19 comments
Labels: enhancement, good first issue

#234 - Error when running cal_abund for a Tax4Fun2 object

Issue - State: closed - Opened by lemv24 over 1 year ago - 2 comments

#233 - Sample data labels replaced with NA after trans_abund

Issue - State: closed - Opened by simeonhebrew over 1 year ago - 4 comments
Labels: enhancement

#232 - Error in cladogram

Issue - State: closed - Opened by Muneer111 over 1 year ago - 5 comments

#231 - heatmap x axis label

Issue - State: open - Opened by apoosakkannu over 1 year ago - 1 comment
Labels: documentation

#230 - venn diagram levels of the factor

Issue - State: open - Opened by apoosakkannu over 1 year ago - 3 comments
Labels: documentation

#229 - number of phylum or class or order in dataset

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

#228 - About plot_bar

Issue - State: closed - Opened by lbwfff over 1 year ago - 1 comment

#222 - Specific color for each treatment (n=6) in plot_diff

Issue - State: closed - Opened by marwa38 over 1 year ago - 8 comments
Labels: enhancement, good first issue

#221 - same color for different levels of a factor in different plots

Issue - State: closed - Opened by apoosakkannu over 1 year ago - 3 comments
Labels: documentation

#220 - saving permanova and beta dispersion results

Issue - State: closed - Opened by apoosakkannu over 1 year ago - 1 comment
Labels: documentation, enhancement

#219 - Reorder x-axis in trans_beta$plot_group_distance issue (version 0.15.0)

Issue - State: closed - Opened by calla404 over 1 year ago - 2 comments
Labels: bug

#218 - No dataset$beta_diversity found!

Issue - State: closed - Opened by koutnymarek over 1 year ago - 4 comments

#216 - Construct and compare with random network

Issue - State: open - Opened by Shawane-Wang over 1 year ago - 8 comments
Labels: enhancement

#215 - Error in tapply(LD, group_vec_lda, mean) : arguments must have same length in "trans_diff"

Issue - State: closed - Opened by marwa38 over 1 year ago - 13 comments
Labels: enhancement

#214 - Query about threads and seeds in cal_powerlaw

Issue - State: closed - Opened by Shawane-Wang over 1 year ago - 2 comments
Labels: enhancement

#213 - Median and IQR for trans_abund

Issue - State: closed - Opened by motroy over 1 year ago - 4 comments
Labels: enhancement

#212 - beta diversity visualisation including most discriminative taxa/genera?

Issue - State: closed - Opened by marwa38 over 1 year ago - 2 comments

#211 - Error in `[.data.frame`(., , apply(., 2, sum) != 0) : 选择了未定义的列

Issue - State: closed - Opened by JBL05 over 1 year ago - 4 comments
Labels: documentation

#210 - beta diversity for a single specific taxa

Issue - State: closed - Opened by guianrey over 1 year ago - 1 comment
Labels: documentation

#209 - Error in is.factor(text) : object 't1' not found in "plot_diff_abund"?

Issue - State: closed - Opened by marwa38 over 1 year ago - 5 comments
Labels: bug

#208 - Welch's t or Wilcoxon tests in "aldex2_t"?

Issue - State: closed - Opened by marwa38 over 1 year ago