SQMtools1.7.2 package

Combine several SQM objects

Combine several SQM or SQMlite objects

Create a bin from a vector of contigs

Export the bins of a SQM object

Export the contigs of a SQM object

Export the taxonomy of a SQM object into a Krona Chart

Export the ORFs of a SQM object

Export the functions of a SQM object into KEGG pathway maps

Export results in tabular format

Find redundant contigs within a bin

Load a SqueezeMeta project into R

Load tables generated by sqm2tables.py, sqmreads2tables.py or `com...

Get the N most abundant rows (or columns) from a numeric table

Get the N most variable rows (or columns) from a numeric table

Plot a barplot using ggplot2

Barplot of the most abundant bins in a SQM object

Heatmap of the most abundant functions in a SQM object

Plot a heatmap using ggplot2

Barplot of the most abundant taxa in a SQM object

Remove contigs from a given bin

Return a vector with the row-wise maxima of a matrix or dataframe.

Return a vector with the row-wise minima of a matrix or dataframe.

Print a named vector of sequences as a fasta-formatted string

Convert a SQM object into a microtable object from the microeco pa...

Convert a SQM object into a phyloseq object from the phyloseq pack...

Create a SQM object containing only the requested bins, and the contig...

Select contigs

Filter results by function

Select ORFs

Select random ORFs

Filter results by sample

Filter results by taxonomy

summary method for class SQM

summary method for class SQMbunch

summary method for class SQMlite