Will Van Treuren
Will Van Treuren
I know QIIME1 support ends soon, but I wanted to record this information somewhere in case people still using it run in to this problem. This also seems like a...
This PR does 3 things: 1. Addresses issue #2061: It changes the way `qiime.filter.filter_mapping_file` behaves to match the documentation. 2. Changes the result `--output_mapping_fp` in `filter_samples_from_otu_table.py`: now writes a subsetted...
using the script `observation_metadata_correlation.py` with `-s cscore` results in failure because the metadata from the mapping file isn't cast as an array. line 2428 needs to change to: ``` python...
I have come across several situations now where the `g_test` in the script `group_significance.py` gives implausibly small p-values. For instance, in a recent forum post, an individual was comparing two...
I propose that `compare_alpha_diversity.py` should follow the format of `group_significance.py` in returning uncorrected AND corrected p-values. Currently, the return looks like (tab separated): `Group1 Group2 Group1 mean Group1 std Group2...
`qiime.filter.filter_mapping_file` is code that needs to be replaced. 1. **Documentation is actively misleading**: documentation says that the function removes metadata columns from the mapping file data if every sample to...
Hi @griquelme - first, thanks for writing `tidyms`, it's a great package. I have been searching for a usable python library to build with. The issue I am currently having...
Working with several different sequencing runs of various qualities I am trying to develop intuition for what reasonable quality filtration parameters are in the function `filterAndTrim`. The relevant parameters are...