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medvir
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VirMet
Set of tools for viral metagenomics.
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Add acc_num to org_list file and modify covplot.py
#53
MaryamZaheri
closed
2 years ago
0
AssertionError
#52
Vikash84
opened
3 years ago
0
Update dbs links and few modifications
#51
MaryamZaheri
closed
4 years ago
0
virmet wolfpack --run doesn't work if run_name starts with a 2
#50
sschmutz
closed
4 years ago
1
virmet covplot not working because of missing ggplot package
#49
mihuber
closed
4 years ago
1
tidytable works with Samples without viral reads
#48
MaryamZaheri
closed
4 years ago
0
read_table is deprecated, use read_csv instead
#47
sschmutz
closed
4 years ago
1
`virmet covplot` for viruses with a segmented genome
#46
sschmutz
opened
5 years ago
1
read count correction and unittest
#45
MaryamZaheri
closed
5 years ago
0
Read counts in orgs_list.tsv is underestimated for some species.
#44
MaryamZaheri
closed
5 years ago
1
virmet readthedocs website not displayed properly
#43
sschmutz
opened
5 years ago
0
if ssciname in unique.tsv is N/A, no entry is written in orgs_list.tsv
#42
sschmutz
closed
5 years ago
0
docker scripts point to wrong ftp addresses for fetching genomes
#41
msegurawang
closed
4 years ago
0
Document hot run capabilities
#40
ozagordi
closed
6 years ago
0
virmet tidytable does not finish if one sample doesn't contain any viral reads
#39
sschmutz
closed
4 years ago
0
Gini index
#38
mihuber
opened
6 years ago
0
Read counts in covplot is overestimated
#37
ozagordi
opened
6 years ago
0
Download taxonomy files
#36
ozagordi
closed
6 years ago
0
Bump to v1.2
#35
ozagordi
closed
6 years ago
0
Update search query to include all viral genomes
#34
ozagordi
closed
6 years ago
0
*coverage.pdf of large genomes not displayed properly
#33
sschmutz
closed
6 years ago
0
add measured variable of coverage and species information
#32
sschmutz
closed
6 years ago
0
wolfpack
#31
LCarioti
closed
6 years ago
12
./ or ../ as --outdir argument in tidytable.py leads to an error
#30
sschmutz
closed
6 years ago
1
Build database virus
#29
Castell34
closed
6 years ago
7
depth.txt is overwritten if you run covplot more than once
#28
sschmutz
closed
6 years ago
1
Virus reads used for alignment covplot
#27
mihuber
closed
6 years ago
1
Version of VirMet and virus reference database
#26
mihuber
closed
6 years ago
4
Quality filtering of NanoPore reads
#25
mihuber
opened
7 years ago
3
Re-analysis of samples
#24
mihuber
closed
6 years ago
2
Fix empty files and update deprecated method in pandas
#23
ozagordi
closed
7 years ago
0
Error when no viral reads are found: AttributeError: 'Series'
#22
ozagordi
closed
7 years ago
1
FileNotFoundError when running single files
#21
mihuber
closed
7 years ago
0
Bug in tidytable
#20
mihuber
closed
7 years ago
0
Write better output for `update`
#19
ozagordi
closed
6 years ago
0
TidyData Table
#18
mihuber
closed
7 years ago
0
FutureDeprecation warning in `covplot.py`
#17
ozagordi
closed
7 years ago
0
Adapt to phase out of genbank identifiers
#16
ozagordi
closed
7 years ago
0
Adapt to phasing out of GI numbers by NCBI.
#15
ozagordi
closed
7 years ago
0
Write `covplot` documentation
#14
ozagordi
closed
8 years ago
0
More aggressive clean up
#13
ozagordi
closed
8 years ago
0
Command to update fungal db, check also bacterial update
#12
ozagordi
closed
8 years ago
0
Matching contaminant
#11
ozagordi
closed
8 years ago
0
Locking strategy
#10
ozagordi
closed
8 years ago
0
Fetching databases in parallel
#9
ozagordi
closed
8 years ago
1
Reporting
#8
mihuber
closed
8 years ago
1
Coverage plot
#7
ozagordi
closed
8 years ago
0
Logging improvements
#6
ozagordi
closed
8 years ago
0
Input
#5
mihuber
closed
8 years ago
0
Output
#4
mihuber
closed
8 years ago
2
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