pavian

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Hi, I'm facing a problem when in try to install pavian in R (4.2.2) with: install.packages("remotes") remotes::install_github("fbreitwieser/pavian") I get: ERROR: dependencies 'sankeyD3', 'shinyFileTree' are not available for package 'pavian' Maybe...

MeCaro1

I wondered why my sankey plot generated using Pavian online tool looks diff from those generated from others and the example files, as the thickness of the lines in my...

evolbeginner

Error rendering graphs

2

From Kraken report uploaded I get this message can you help? [Mar06 16:05] Started new shiny session #1 (1 session(s) running) [Mar06 16:06] Reading files in C:/Users/mdg.bio/AppData/Local/Temp/Rtmpo9PGeX/b51bd21ee452dffe5779957c [Mar06 16:06] Reading...

turbo4xl

Errors when comparing across samples

4

Hi, When I combine MetaPhlan 3 reports with Kraken / Centrifuge ones, I get an error at the across samples plot under the sample tab when clicking a specific taxon...

pieterjanvc

sankey vizualization

1

Hi i am a evolutionary biology guy. I loved the sankey visualization in pavian. is there any way to make this vizualization directly from taxid and scientific name? with cool...

Yogesh1-11

Hello, we have analyzed 16S amplicon data with Kraken2 and subsequent Bracken quantification, Both report files could be imported to Pavian, but the Bracken report files do not display any...

ARW-UBT

Making sankey figure for classification outputs from GTDB-Tk

2

Dear pavian support team, I am trying to make one sankey figure for my classification output - **gtdbtk.bac120.summary.tsv.txt**, I also transferred the gtdbtk.bac120.summary.tsv to format like **gtdbtk_bac120_summary.tsv.txt**. But, both don't...

B-1991-ing

Pavian with amplicon sequencing data

1

Hi, Is there a way to use Pavian with amplicon sequencing data (e.g. 16S or 18S)? Best, Sam

slambrechts

kaiju to pavian

2

Re: issue #11 Is there an updated script available to convert kaiju outputs into the correct "kreport"-styled input format for pavian (given that the kraken-report has been replaced by kaiju2table...

dnlrxn

Is there a way to share the generated interactive pavian output

1

Hi everyone! I've run pavian both from R or directly from the webpage (which in the end is the same), the output is great with the added interactivity, I would...

alanxelena