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Feature | Fetch data from Metalog and create a TSE object #814

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Feature | Fetch data from Metalog and create a TSE object #814

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dfc1a10
refactor to fit mia style
raivo-otus Apr 2, 2026
c795a72
Add phylogeny tree
raivo-otus Apr 7, 2026
a672a20
use dense matrix assays for better support
raivo-otus Apr 7, 2026
156e4e1
feature to combine multiple as sparse and make dense later
raivo-otus Apr 8, 2026
2b0370d
Merge branch 'microbiome:devel' into feat/create-metalog-tse
raivo-otus Apr 30, 2026
4c63db2
Merge branch 'devel' into feat/create-metalog-tse
raivo-otus Jun 10, 2026
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13 changes: 13 additions & 0 deletions ..Rcheck/00check.log
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Original file line number Diff line number Diff line change
@@ -0,0 +1,13 @@
* using log directory ‘/home/rpth/Projects/mia/..Rcheck’
* using R version 4.5.3 (2026-03-11)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04.3) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04.3) 11.4.0
* running under: Pop!_OS 22.04 LTS
* using session charset: UTF-8
* checking for file ‘./DESCRIPTION’ ... ERROR
Required fields missing or empty:
‘Author’ ‘Maintainer’
* DONE
Status: 1 ERROR
3 changes: 3 additions & 0 deletions DESCRIPTION
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Expand Up @@ -67,14 +67,17 @@ Imports:
BiocParallel,
Biostrings,
bluster,
data.table,
DECIPHER,
decontam,
DelayedArray,
DelayedMatrixStats,
DirichletMultinomial,
dplyr,
httr2,
IRanges,
MASS,
Matrix,
MatrixGenerics,
methods,
ecodive,
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19 changes: 19 additions & 0 deletions NAMESPACE
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Expand Up @@ -57,6 +57,7 @@ export(estimateDominance)
export(estimateEvenness)
export(estimateFaith)
export(estimateRichness)
export(fetchMetalogTSE)
export(full_join)
export(getAbundanceClass)
export(getAbundant)
Expand Down Expand Up @@ -362,6 +363,8 @@ importFrom(IRanges,LogicalList)
importFrom(IRanges,NumericList)
importFrom(IRanges,relist)
importFrom(MASS,isoMDS)
importFrom(Matrix,rowSums)
importFrom(Matrix,sparseMatrix)
importFrom(MatrixGenerics,rowSums2)
importFrom(MultiAssayExperiment,ExperimentList)
importFrom(MultiAssayExperiment,MultiAssayExperiment)
Expand Down Expand Up @@ -401,6 +404,7 @@ importFrom(SummarizedExperiment,assays)
importFrom(SummarizedExperiment,colData)
importFrom(SummarizedExperiment,rowData)
importFrom(SummarizedExperiment,rowRanges)
importFrom(TreeSummarizedExperiment,TreeSummarizedExperiment)
importFrom(TreeSummarizedExperiment,changeTree)
importFrom(TreeSummarizedExperiment,subsetByLeaf)
importFrom(ape,as.phylo)
Expand All @@ -414,6 +418,11 @@ importFrom(ape,is.rooted)
importFrom(ape,read.tree)
importFrom(ape,reorder.phylo)
importFrom(bluster,clusterRows)
importFrom(data.table,dcast)
importFrom(data.table,fread)
importFrom(data.table,setkey)
importFrom(data.table,setnames)
importFrom(data.table,tstrsplit)
importFrom(decontam,isContaminant)
importFrom(decontam,isNotContaminant)
importFrom(dplyr,"%>%")
Expand All @@ -432,6 +441,16 @@ importFrom(dplyr,sym)
importFrom(dplyr,tally)
importFrom(ecodive,unweighted_unifrac)
importFrom(ecodive,weighted_unifrac)
importFrom(httr2,req_error)
importFrom(httr2,req_options)
importFrom(httr2,req_perform)
importFrom(httr2,req_progress)
importFrom(httr2,req_retry)
importFrom(httr2,req_timeout)
importFrom(httr2,req_user_agent)
importFrom(httr2,request)
importFrom(httr2,resp_header)
importFrom(httr2,resp_status)
importFrom(rlang,":=")
importFrom(rlang,sym)
importFrom(scater,calculateMDS)
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