arendsee / phylostratr

An R framework for phylostratigraphy

arendsee/phylostratr Issues

"ncbi_tree" function error: Error in x$id : $ operator is invalid for atomic vectors
Updated a year ago1
Error: The focal species is not present in UniProt
Updated a year ago3
strata_blast issue
Closed 4 years ago18
Error in (function (fastafile, blastdb = "blastdb", verbose = FALSE) : Failed to make blast database blastdb/Araport11_genes.201606.pep.fasta In addition: Warning message: In system2("makeblastdb", stderr = TRUE, stdout = TRUE, args = c("-dbtype", : running command '"makeblastdb" -dbtype prot -in Araport11_genes.201606.pep.fasta -out blastdb/Araport11_genes.201606.pep.fasta' had status 1
Updated a year ago10
Error in if (class(strata) != "Strata") { : the condition has length > 1
Updated a year ago1
Error in readLines(con) : HTTP error 400.
Closed 2 years ago14
Help!!!! HTTP 400
Closed 2 years ago1
May I use Phylostratr to study the genomic phylostratigraphy of Mycobacterium tuberculosis?
Updated 2 years ago
Let phylostratr read blast outputs directly!
Closed 6 years ago5
Error when importing external blast results
Updated 3 years ago
strata_blast issue, similar to #15
Updated 3 years ago
Duplicated factor levels while calling stratify()
Updated 4 years ago
No alias or index file found
Updated 4 years ago
Error: 'classification' is not an exported object from 'namespace:taxizedb'
Closed 4 years ago1
qseqid problem
Closed 4 years ago8
BLAST Database error
Updated 4 years ago3
[Question]NCBI nr database VS uniprot
Closed 4 years ago1
Empty faa file for 1008392 produces error with diamond
Closed 4 years ago2
Heatmap layout
Updated 5 years ago8
Issues in compiling results
Updated 5 years ago
Issue in compiling phylostratr results
Closed 5 years ago2
Invalid Strata object
Updated 5 years ago8
swap `BiocInstaller` with `BiocManager`
Closed 5 years ago8
Error (?) - strata_besthits
Closed 6 years ago2
Possible bug? number of genes per strata is way higher than the total number of genes
Closed 6 years ago20
Cannot resolve tree ids in `merge_besthits`
Closed 6 years ago15
How much local storage does it normally take?
Closed 6 years ago2
Installation issue: phylostratr is fully compatible only with latest ggtree and treeio
Closed 6 years ago4