Owner

grunwaldlab

3 indexed repositories · View on GitHub

metacoder
Parsing, Manipulation, and Visualization of Metabarcoding/Taxonomic data

R · 148 stars
Population_Genetics_in_R
A primer for computational tools to analyze genetics of populations in R

HTML · 92 stars
PathoSurveilR
Tools to find and manipulate the output of pathogensurveillance

R · 3 stars

Beginner friendly Everything

Open All

Add functions to calculate and plot files space used by various outputs Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 20/100

grunwaldlab/PathoSurveilR#18 · Opened Jul 17, 2025
Static minimum spanning network plotting Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

grunwaldlab/PathoSurveilR#17 · Opened Mar 17, 2025
Using ANCOM-BC2 for DA analysis Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

grunwaldlab/metacoder#364 · Opened Jul 29, 2024
Map of samples Open

grunwaldlab/PathoSurveilR#14 · 1 assignee · Opened Feb 13, 2024
Interactive minimum spanning network function Open

grunwaldlab/PathoSurveilR#11 · 1 assignee · Opened Jan 11, 2024
Interactive tree drawing function Open

grunwaldlab/PathoSurveilR#7 · 1 assignee · Opened Jan 11, 2024
calc_diff_abund_deseq2, linear variables and "design"? Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

grunwaldlab/metacoder#351 · 3 comments · Opened Aug 9, 2023
ggtext compatibility Open

Difficulty 5/5 Over a week Newbie friendliness 20/100

grunwaldlab/metacoder#347 · 2 comments · Opened Mar 27, 2023
italicize node labels? Open

Difficulty 3/5 1-2 days Newbie friendliness 25/100

grunwaldlab/metacoder#345 · 2 comments · Opened Jan 25, 2023
Feedback after following the primer Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

grunwaldlab/Population_Genetics_in_R#44 · Opened Jun 15, 2022
Error in repel_boxes(data_points = as.matrix(text_data[movable, c("x", : std::bad_alloc Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

grunwaldlab/metacoder#338 · Opened May 18, 2022
Update example data format Open

Difficulty 2/5 1-3 hours Newbie friendliness 25/100

grunwaldlab/metacoder#331 · 2 reactions · Opened Feb 2, 2022
ggrepel advanced options Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

grunwaldlab/metacoder#303 · 1 comment · Opened Mar 11, 2021
heat_tree_matrix Error: Error in apply(layout_matrix, MARGIN = 2, function(x) all(is.na(x))) : dim(X) must have a positive length Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

grunwaldlab/metacoder#301 · 4 comments · Opened Mar 8, 2021
heat_tree_matrix title Open

Difficulty 3/5 1-2 days Newbie friendliness 25/100

grunwaldlab/metacoder#296 · 1 comment · Opened Dec 17, 2020
Multiple heat tree comparisons against a single reference treatment Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

grunwaldlab/metacoder#292 · 3 comments · Opened Sep 4, 2020
Different Node Shapes? Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

grunwaldlab/metacoder#284 · 2 comments · Opened Apr 29, 2020
Add new quote to home page Open

Difficulty 1/5 Under an hour Newbie friendliness 54/100

grunwaldlab/Population_Genetics_in_R#41 · 1 comment · Opened Dec 4, 2019
Make clalc_taxon_abund work with presence/absence data Open

Difficulty 3/5 1-2 days Newbie friendliness 25/100

grunwaldlab/metacoder#267 · 4 comments · Opened Jun 27, 2019
heat_tree legend size Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

grunwaldlab/metacoder#265 · 4 comments · Opened Jun 7, 2019
Creating a facet with multiple heat trees Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

grunwaldlab/metacoder#263 · 15 comments · Opened Apr 14, 2019
Thoughts on heat_tree argument formats Open

Difficulty 5/5 Over a week Newbie friendliness 20/100

grunwaldlab/metacoder#260 · 4 comments · 1 reaction · Opened Jan 16, 2019
(nanhwe.pop <- seppop(nancycats) %>% lapply(hw.test, B = 0)) not working Open

Difficulty 4/5 3-5 days Newbie friendliness 30/100

grunwaldlab/Population_Genetics_in_R#38 · 1 comment · Opened Sep 18, 2018
Color legend Open

Difficulty 4/5 3-5 days Newbie friendliness 42/100

grunwaldlab/metacoder#242 · 1 comment · Opened Jul 19, 2018
Add apply and sweep to appendix Open

Difficulty 2/5 1-3 hours Newbie friendliness 48/100

grunwaldlab/Population_Genetics_in_R#31 · 1 reaction · Opened Jun 19, 2018
heat_tree: Make error for when a taxmap object is passed to wrong parameter Open

heat tree rewrite

Difficulty 3/5 1-2 days Newbie friendliness 45/100

grunwaldlab/metacoder#231 · Opened Apr 27, 2018
Add warning message when heat_tree cannot pick good size range Open

heat tree rewrite

Difficulty 3/5 1-2 days Newbie friendliness 35/100

grunwaldlab/metacoder#213 · Opened Feb 5, 2018
Adding color to nodes based on specific values of observations. Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

grunwaldlab/metacoder#210 · 11 comments · Opened Feb 1, 2018
Look into treeio for parsing phylogenetic file formats Open

Priority: High Status: Pending Type: Enhancement

Difficulty 4/5 3-5 days Newbie friendliness 20/100

grunwaldlab/metacoder#208 · Opened Jan 29, 2018
consider functions for alpha/beta diversity per taxon Open

Priority: High Status: In Progress Type: Enhancement

Difficulty 5/5 Over a week Newbie friendliness 25/100

grunwaldlab/metacoder#207 · Opened Jan 23, 2018
heat_tree_matrix assumes default color scale Open

Status: On Hold Type: Bug

Difficulty 3/5 1-2 days Newbie friendliness 35/100

grunwaldlab/metacoder#196 · 4 comments · Opened Jan 10, 2018
Add function to make nested stacked barcharts Open

Priority: Low Status: On Hold Type: Enhancement

grunwaldlab/metacoder#193 · 1 assignee · Opened Jan 5, 2018
Add function to visualize primer mismatch to binding sites Open

someday

Difficulty 5/5 Over a week Newbie friendliness 30/100

grunwaldlab/metacoder#192 · Opened Jan 3, 2018
Add heat_tree option to scale legend text size Open

heat tree rewrite

Difficulty 4/5 3-5 days Newbie friendliness 20/100

grunwaldlab/metacoder#176 · Opened Oct 11, 2017
Look into using the USEARCH "search_pcr" command for in silico PCR Open

Difficulty 5/5 Over a week Newbie friendliness 20/100

grunwaldlab/metacoder#175 · Opened Sep 21, 2017
Different ploidy examjples Open

Difficulty 4/5 3-5 days Newbie friendliness 30/100

grunwaldlab/Population_Genetics_in_R#27 · Opened Aug 22, 2017
Add exercises to genomics and GBS sections Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

grunwaldlab/Population_Genetics_in_R#26 · 4 comments · Opened Aug 22, 2017
filter_taxa collides with command in phyloseq package Open

Difficulty 1/5 1-3 hours Newbie friendliness 45/100

grunwaldlab/metacoder#170 · 1 comment · Opened Aug 18, 2017
Add parser for SILVA taxonomy files Open

Priority: Medium Status: On Hold Type: Enhancement

Difficulty 4/5 3-5 days Newbie friendliness 25/100

grunwaldlab/metacoder#166 · Opened Aug 2, 2017
Look into ape nexus parser/converter Open

Priority: Medium Status: On Hold Type: Enhancement

Difficulty 4/5 3-5 days Newbie friendliness 25/100

grunwaldlab/metacoder#165 · Opened Aug 1, 2017
Add parser for GenBank taxonomy database Open

Difficulty 4/5 3-5 days Newbie friendliness 20/100

grunwaldlab/metacoder#163 · Opened Jul 31, 2017
Look into cophylo plots once branch length is added Open

someday

Difficulty 5/5 Over a week Newbie friendliness 20/100

grunwaldlab/metacoder#148 · Opened Jul 18, 2017
Update appendix Open

Difficulty 3/5 1-2 days Newbie friendliness 20/100

grunwaldlab/Population_Genetics_in_R#24 · Opened Jul 17, 2017
preGenomics_backup Open

Difficulty 1/5 Under an hour Newbie friendliness 10/100

grunwaldlab/Population_Genetics_in_R#22 · Opened Jul 17, 2017
Best practice to parse data from QIIME Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

grunwaldlab/metacoder#135 · 4 comments · Opened Mar 13, 2017
Add parser for nested strucutres Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

grunwaldlab/metacoder#130 · Opened Aug 29, 2016
aboot with hierfstat::fstat Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

grunwaldlab/Population_Genetics_in_R#21 · Opened Aug 11, 2016
Add option to change rotation of vertex labels Open

Difficulty 4/5 3-5 days Newbie friendliness 20/100

grunwaldlab/metacoder#125 · Opened Aug 8, 2016
Explore using bookdown for rendering the site Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 25/100

grunwaldlab/Population_Genetics_in_R#20 · 1 reaction · Opened Jul 7, 2016
Make standard stacked barcharts Open

Difficulty 5/5 Over a week Newbie friendliness 35/100

grunwaldlab/metacoder#105 · Opened May 26, 2016

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