issues
search
wilkelab
/
cinful
A fully automated pipeline to identify microcins along with their associated immunity proteins and export machinery
GNU General Public License v3.0
6
stars
1
forks
source link
issues
Newest
Newest
Most commented
Recently updated
Oldest
Least commented
Least recently updated
Fix installation instructions
#57
AaronFeller
closed
7 months ago
0
Fix best hits output for immunity proteins
#56
AaronFeller
closed
2 years ago
0
Fix setup_dbs.smk to produce corect pephash.csv files
#55
AaronFeller
closed
2 years ago
0
Update microcins.verified.pep for input
#54
AaronFeller
closed
2 years ago
0
Fixed two issues and cleaned up code in other places.
#53
AaronFeller
closed
2 years ago
0
Update to codebase for publication
#52
AaronFeller
closed
2 years ago
0
verified_directory
#51
AaronFeller
closed
2 years ago
0
support gzipped assemblies
#50
tijeco
closed
2 years ago
1
Exact match to verified dataset
#49
tijeco
closed
3 years ago
0
add support for neubi
#48
tijeco
closed
1 year ago
1
MFP submodule
#47
tijeco
closed
2 years ago
0
update for 0.1.0
#46
tijeco
closed
3 years ago
0
Generate data for unit tests with updated routines
#45
tijeco
closed
1 year ago
1
Cinful
#44
tijeco
closed
3 years ago
0
pass snakemake arguments to cinful
#43
tijeco
closed
1 year ago
1
cinful_id instead of Unnamed: 0
#42
tijeco
closed
3 years ago
1
too many files in python package
#41
tijeco
closed
2 years ago
0
rearrange merge (closes #39)
#40
tijeco
closed
3 years ago
1
Rearrange merge with blast results and nr prodigal file
#39
tijeco
closed
3 years ago
1
Migrate cinful/notebooks to docs/notebooks
#38
tijeco
closed
2 years ago
1
output fasta files
#37
tijeco
closed
3 years ago
0
python wrapper / package
#36
tijeco
closed
3 years ago
0
signal match 3 orfs upstream and downstream of CvaB
#35
tijeco
opened
3 years ago
1
use seqkit for nonredundant prodigal
#34
tijeco
opened
3 years ago
0
nonredundant_prodigal sample unit test
#33
tijeco
closed
3 years ago
0
github action needs cinful environment activated in unit test block
#32
tijeco
closed
3 years ago
0
allows for configuration closes #30
#31
tijeco
closed
3 years ago
0
configuration
#30
tijeco
closed
3 years ago
2
Run individual rules
#29
tijeco
closed
3 years ago
0
Add signalMatch start and stop to output
#28
tijeco
opened
3 years ago
1
add signalSeq HMM to final output
#27
tijeco
closed
3 years ago
0
Signal search HMM needs to be put in different location
#26
tijeco
closed
3 years ago
0
input format and extention
#25
tijeco
closed
2 years ago
1
benchmark
#24
tijeco
closed
3 years ago
0
support for one thread with max_threads
#23
tijeco
closed
3 years ago
0
CvaB search with multithreaded diamond instead of blastp
#22
tijeco
closed
3 years ago
0
multithread blastp
#21
tijeco
closed
3 years ago
0
more strict CvaB pre-filter length
#20
tijeco
closed
3 years ago
0
component snakefiles
#19
tijeco
closed
3 years ago
0
final output file with best hits for all three components
#18
tijeco
closed
3 years ago
0
pick best blast hit for cvab
#17
tijeco
closed
3 years ago
1
catalytic triad of best cvab hit or maybe all hits using mafft add
#16
tijeco
closed
3 years ago
1
pyhmmer microcin signal sequence search
#15
tijeco
closed
3 years ago
0
tmhmmPY for immunity protein
#14
tijeco
closed
3 years ago
1
all output should be placed in one directory, with subdirectories.
#13
tijeco
closed
3 years ago
0
Make a single duomolog/blast/hmmer snakefile
#12
tijeco
closed
3 years ago
0
other Klebsiella refseq assemblies
#11
tijeco
closed
3 years ago
0
Klebsiella pneumoniae refseq assemblies
#10
tijeco
closed
3 years ago
0
Other Escherichia refseq assemblies
#9
tijeco
closed
3 years ago
0
E. coli refseq assemblies
#8
tijeco
closed
3 years ago
0
Next