Iva Veseli

Add lambda parameter for q-value estimation in enrichment script

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This PR addresses an issue discovered [here](https://github.com/merenlab/anvio/issues/1383#issuecomment-1169142656), whereby very small p-values would lead to an ugly `seq` bug like this: ``` Error in seq.default(0.05, max_lambda, 0.05) : wrong sign in...

[FEATURE] anvi-estimate-scg-taxonomy should accept external/internal genomes file

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## The need If you want to estimate taxonomy on a lot of different genomes, right now the only way is to run `anvi-estimate-scg-taxonomy` one at a time on each...

[BUG] Anvi'o should check write permissions of databases before doing computationally expensive work

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## Short description of the problem When running `anvi-run-kegg-kofams` (or other computationally expensive operations that require writing to a database at the end of it), anvi'o doesn't check if you...

## The need This is applicable mostly to metagenomics (and manual mode) in `anvi-interactive`. As I understand it, we currently can normalize coverage data by the number of reads mapping...

This PR adds the script `anvi-script-classify-hmi-genomes`, which can tell the user if their provided genome has high metabolic independence (HMI) or low metabolic independence (LMI). The way we score the...

[DISCUSSION] Common misconceptions and mistakes for anvi'o beginners that we should clarify in a blog post

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@FlorianTrigodet and I have noticed several common issues emerging from recent Discord questions. These are not really bugs, but quirks of the anvi'o ecosystem that are not obvious to beginners....

[FEATURE REQUEST] Outputs for function- and pathway-level variability analysis

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## The need I am opening this issue on behalf of @tdelmont, who wants a strategy that connects the SNV and SAAV data stored in the profile database to functions...

[BUG] Most annotations from anvi-run-cazymes have undefined ('-') accession numbers

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## Short description of the problem When we annotate a contigs database with `anvi-run-cazymes`, most of the resulting hits in the gene functions table have `-` for an accession value:...

[FEATURE REQUEST] Adding a program to annotate viral PHROGs via their HMMs

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A small project to improve anvi'o, based upon feedback/ideas @FlorianTrigodet and I heard from our colleagues at the QIB in Norwich. ## The need The [PHROGs database](https://phrogs.lmge.uca.fr/) contains orthologous groups...

[FEATURE REQUEST] A conda package for anvi'o with a minimal installation option

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A small project to improve anvi'o, based upon feedback/ideas @FlorianTrigodet and I heard from our colleagues at the QIB in Norwich. ## The need Some people might benefit from a...