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bowmanjeffs
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paprica
paprica - PAthway PRediction by phylogenetIC plAcement
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Benchmarking against PICRUst/Tax4fun?
#51
GeoMicroSoares
closed
7 years ago
1
HMM banded truncated alignment
#50
lucaz88
closed
5 years ago
6
Virtual box
#49
AnweshaGhosh
closed
7 years ago
1
test flag
#48
bowmanjeffs
opened
7 years ago
0
Speed up PAPRICA by only using unique sequences?
#47
chassenr
closed
7 years ago
1
taxid for draft genomes in paprica-place_it
#46
bowmanjeffs
closed
3 years ago
0
paprica-mt ouput needs taxid and taxa name
#45
bowmanjeffs
opened
7 years ago
0
include proteins without EC numbers (e.g. KO)
#44
bowmanjeffs
opened
7 years ago
0
Eukaryote
#43
bowmanjeffs
closed
7 years ago
0
MAP data in tally_pathways
#42
bowmanjeffs
closed
7 years ago
0
classification
#41
bowmanjeffs
closed
7 years ago
0
error in ./paprica-run.sh test.bacteria bacteria
#40
chassenr
closed
7 years ago
7
paprica mg, Error: Incompatible database version
#39
blancaverag
closed
7 years ago
4
raxml version needs to be changed in paprica-make_ref.py too
#38
blancaverag
closed
7 years ago
3
better behavior for unique 16S reps
#37
bowmanjeffs
opened
7 years ago
0
id pgdbs created for draft genomes
#36
bowmanjeffs
opened
8 years ago
0
fix n16S genes for draft genomes
#35
bowmanjeffs
opened
8 years ago
0
pplacer reference package
#34
bowmanjeffs
closed
7 years ago
0
add biom formatted output
#33
bowmanjeffs
closed
7 years ago
0
input file for known missing EC
#32
bowmanjeffs
closed
7 years ago
1
provide outgroup for trees
#31
bowmanjeffs
closed
7 years ago
0
v0.3.0
#30
bowmanjeffs
closed
8 years ago
0
In paprica_build.sh, "paprica_place_it.py", line 166... KeyError 'ref'
#29
karoraw1
closed
8 years ago
3
add cutoff variable as flag to tally_pathways
#28
bowmanjeffs
closed
8 years ago
0
some way of versioning the database is necessary
#27
bowmanjeffs
closed
8 years ago
1
tally_pathways naming
#26
bowmanjeffs
closed
8 years ago
0
include binaries
#25
bowmanjeffs
closed
8 years ago
1
V0.22.2
#24
bowmanjeffs
closed
8 years ago
0
V0.22.1
#23
bowmanjeffs
closed
8 years ago
0
paprica_build_core_genomes is generating blank dataframes
#22
bowmanjeffs
closed
8 years ago
1
RAxML_distances.dist is missing
#21
karoraw1
closed
8 years ago
4
Dependencies list in PAPRICA_manual_v0.20.pdf
#20
karoraw1
closed
8 years ago
0
paprica_build.sh unknown error
#19
karoraw1
closed
8 years ago
13
sample_data
#18
bowmanjeffs
closed
7 years ago
0
change default cutoff variable
#17
bowmanjeffs
closed
8 years ago
0
some edges missing entries in genome_data_final.csv
#16
bowmanjeffs
closed
8 years ago
0
wget
#15
bowmanjeffs
closed
7 years ago
0
profile
#14
bowmanjeffs
closed
8 years ago
0
Archaea
#13
bowmanjeffs
closed
8 years ago
1
Add GC content as an evaluated parameter
#12
bowmanjeffs
closed
8 years ago
0
Utility for PGDB creation
#11
bowmanjeffs
closed
3 years ago
0
output directory
#10
bowmanjeffs
closed
8 years ago
1
Prediction of genome parameters for internal nodes
#9
bowmanjeffs
opened
8 years ago
0
Change to multigene alignment
#8
bowmanjeffs
closed
3 years ago
1
Change alignment method
#7
bowmanjeffs
closed
8 years ago
0
Change16S find method
#6
bowmanjeffs
closed
8 years ago
0
Eliminate Archaea
#5
bowmanjeffs
closed
8 years ago
0
tar -xzvf issue in shell scripts
#4
bowmanjeffs
closed
8 years ago
0
Specify output database
#3
bowmanjeffs
closed
8 years ago
0
Database version numer incompatability
#2
bowmanjeffs
closed
8 years ago
0
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