`metabaR` external data

This folder is a repository of external resources and toy data examples for the R package metabaR:

SILVA Taxonomy

release 138.1 : tax_slv_ssu_138.1.txt

Raw data tables for the `soil_euk` dataset

Basic table inputs

litiere_euk_reads.txt:
A PCR (rows) by OTU (columns) table: amount of reads of each OTU in each PCR.
litiere_euk_motus.txt:
A OTU (rows) by OTU information (columns) table: e.g. taxonomy, sequence, etc.
litiere_euk_pcrs.txt:
A PCR (rows) by PCR information (columns) table: e.g. PCR plate coordinates, primers used, etc.
litiere_euk_samples.txt:
A sample (rows) by sample information (columns) table: e.g. geographic coordinates.

Obitools inputs

litiere_euk_cl97_agg_filt_tax.tab:
A OTU/seq (rows) by OTU informations (columns; including # reads in a given sample, taxonomy, sequence, etc.). Typically an output from obitools (obitab).
ngsfilter_GWM-768.new_2.txt:
A PCR (rows) by PCR information (columns; any PCR related metadata). Typically a ngsfilter txt file.
Litiere_sample_list_2.txt:
A sample (rows) by sample information (columns; any metadata for samples)

BIOM input

litiere_euk_reads_hdf5.biom:
Soil_euk dataset in the BIOM format.

SILVAngs outputs

lit_euk---ssu---otus.csv:
A file containing taxonomic assignments for each sequence submitted to SILVAngs
lit_euk---ssu---sequence_cluster_map---litiere_euk_cl97_agg_filt.clstr:
A file containing the mapping of each sequence submitted to SILVAngs. Even if no clustering is supposed to be done (i.e. sequence similarity set at 100% in the pipeline), sequences that are strict suffix/prefix of another can still be clustered together with the clustering algorithm used by SILVAngs (CD-HIT).

The `karst_euk` dataset

karst_euk.rds:
A metabarlist corresponding to the karst_euk dataset. To be loaded using the readRDS function.

The `h20_plants` dataset

h20_plants.rds:
A metabarlist corresponding to the h20_plants dataset. To be loaded using the readRDS function.