metacoder

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heat_tree_matrix does not find the needed data

2

Hello, I'm new user of metacoder() and has been following the workshop material "Analysis of Microbiome Community Data in R" Thanks for making the examples available! > library(metacoder) Loading required...

consueloau

calc_diff_abund_deseq2

12

Hi, First of all thanks for developing this amazing package! I would like to use DeSeq2 negative binomial analysis for differential abundance and then use compare_groups and lastly plot a...

rogarcia1992

calc_obs_prop returns Nan when whole column is 0.

1

Would be more convenient to return 0 for the whole column, even if `0/0 = Nan`

zachary-foster

Heat tree matrix error: could not find function "parse_dataset"

2

Hi, Thank you for a great package! I really like the heat trees and I would like to use the heat_tree_matrix() function to compare different groups in my dataset, but...

Tre10

Multiple heat tree comparisons against a single reference treatment

3

It would be very good if we could define one specific condition as control and plot all against this single condition. I couldn´t find a way in the documentation, is...

marcelladane

Running in paralle or multithreading option

2

Hey there.. Thanks the nice tool. Is there a way to run the final matrix in a parallel or multi-threaded manner. I have the following with a lot of rows...

susheelbhanu

Make clalc_taxon_abund work with presence/absence data

4

zachary-foster

Metacoder continuous variable function for longitudinal dataset

2

Hi Zach, I have a shotgun metagenomic sequencing dataset consisting of 17 patients that have daily vaginal microbiome samples for a period of 21 days post surgical obstetric fistula repair,...

MADscientist314

parse_phyloseq and n_obs as node_size question

8

Hi, I am just started to work with metacoder, but I have a simple question. When I import a phyloseq object with parse phyloseq I can see the all components...

pedres

Different Node Shapes?

2

Hi Zach, I was wondering if there is a way to set the node shapes. I saw it on a future development list and wondered if you had some code...

noelzach