biocore DEICODE issues - Githubissues

biocore / DEICODE

Robust Aitchison PCA from sparse count data

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DEICODE toy tutorial not working in qiime2-amplicon-2024.5 version

#68 magibc opened 1 month ago
0
For current version of Qiime2, fix bugs or highlight deprecation

#67 colinbrislawn opened 7 months ago
1
(1/1) Invalid value for '--i-table': 'kelp-biom.qza' is not a QIIME 2 Artifact (.qza)

#66 scleractinia closed 8 months ago
1
segmentation fault

#65 nvpatin opened 2 years ago
12
Update readme with update for future of package

#64 cameronmartino closed 2 years ago
0
update branch

#63 cameronmartino closed 2 years ago
0
DEICODE Package for R Programming Language

#62 erfanshekarriz opened 2 years ago
1
converting otu_table.csv format to otu_table.qza

#61 Hesham999666 opened 3 years ago
1
Still having issue with arrow bias in biplot

#60 manasson opened 4 years ago
1
Produce robust clr matrix as output.

#59 davised opened 4 years ago
6
add paper citation

#58 gwarmstrong opened 4 years ago
0
Does DEICODE meet the assumption of same "multivariate spread" among groups for PERMANOVA?

#57 Jigyasa3 opened 4 years ago
1
arrows appear to be biased?

#56 scher-lab closed 4 years ago
4
autorpca returns a column full of zeros

#55 mortonjt closed 4 years ago
2
bug fixes in ordering and fraction total variance explained

#54 cameronmartino closed 4 years ago
5
fraction variance explained.

#53 cameronmartino closed 4 years ago
1
"variation of interest" seems to be split across axis 2 instead of axis 1, as expected?

#52 fedarko closed 4 years ago
4
collapse the deicode distance matrix back into feature tables before rpca function?

#51 Jigyasa3 opened 5 years ago
1
Is there a recommended value for "--min-sample" count and "--min-feature" count?

#50 Jigyasa3 closed 5 years ago
5
Error-k must be between 1 and min(A.shape). What is k?

#49 Jigyasa3 closed 5 years ago
2
pip install and setup.py doesn't install DEICODE on computing cluster

#48 Jigyasa3 closed 5 years ago
4
Applying it on shot-gun metagenome data without microbial phylogeny info

#47 Jigyasa3 closed 5 years ago
10
How to use OptSpace function in Python? No fit_transform method

#46 jolespin opened 5 years ago
6
Add frequency filter.

#45 cameronmartino closed 4 years ago
1
changing matplotlib backend

#44 mortonjt closed 5 years ago
3
Typo in tutorial

#43 mortonjt closed 5 years ago
0
Add version check in command line

#42 cameronmartino opened 5 years ago
1
Make docs consistent re: default/min parameters

#41 fedarko opened 5 years ago
2
Update the tutorial output with the changes made in PR #36 & #38.

#40 cameronmartino closed 5 years ago
1
Add emperor mchelper with CF data

#39 cameronmartino opened 5 years ago
0
Fixes the centering issue

#38 mortonjt closed 5 years ago
8
The centering issue remains

#37 mortonjt closed 5 years ago
3
Adding tests, documentation, arrow scaling issue

#36 cameronmartino closed 5 years ago
4
Fix a docstring in the Q2 test code

#35 fedarko closed 5 years ago
0
Sorting eigenvalues and accompanying tests

#34 cameronmartino closed 5 years ago
3
fix eigenvalues order issue

#33 cameronmartino closed 5 years ago
1
proportion explained / eigenvalues are swapped

#32 mortonjt closed 5 years ago
2
update matrix handling to scipy 2-D sparse

#31 cameronmartino opened 5 years ago
0
Maximum recursion depth exceeded

#30 justinshaffer closed 5 years ago
5
Refactor redundant code between standalone and QIIME 2 RPCA methods

#29 fedarko closed 5 years ago
18
Duplicated Scripts

#28 cameronmartino closed 5 years ago
0
Center biplot

#27 cameronmartino closed 5 years ago
4
Biplot arrows not completely centered

#26 mortonjt closed 5 years ago
1
Fix broken links

#25 cameronmartino closed 5 years ago
2
broken image links in tutorial

#24 mestaki closed 5 years ago
1
Change tutorial dataset to "moving pictures"

#23 cameronmartino closed 5 years ago
1
QIIME error

#22 cameronmartino closed 5 years ago
2
Update tutorials and add distance

#21 cameronmartino closed 5 years ago
2
conda install in qiime2-2018.11

#20 cameronmartino closed 5 years ago
4
Update readme

#19 cameronmartino closed 5 years ago
0