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lenaschimmel
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sc2rf
SARS-Cov-2 Recombinant Finder for fasta sequences
MIT License
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Bug/question with --force-all-parents --clades all
#35
MarieLataretu
opened
2 years ago
3
Bridging the gap between sc2rf result and Pangolin X* lineages
#34
bioinforME
opened
2 years ago
0
Minor changes to readme for version
#33
SVN-PhD
opened
2 years ago
0
How to interpret BA.4/BA.5 list of mutations
#32
jpflorido
opened
2 years ago
0
GISAID XT recombinant not detected by sc2rf
#31
BenjaminDelisle
opened
2 years ago
4
Option to ignore shared substitutions
#30
ktmeaton
opened
2 years ago
0
Terminal Ns not recognized as missing
#29
ktmeaton
opened
2 years ago
1
--csvfile option does not work
#28
think-o
closed
2 years ago
2
Crash related to tdqm
#27
lenaschimmel
closed
2 years ago
4
ENH: Sort by breakpoint
#26
corneliusroemer
opened
2 years ago
0
Proposed fix for #19 - output CSV
#25
ArtPoon
closed
2 years ago
13
ENH: Accept MAPLE file as alternative to fasta
#24
corneliusroemer
opened
2 years ago
0
BUG: Problem using covSpectrum mutation share - Ns are treated as reference
#23
corneliusroemer
closed
2 years ago
10
ENH: Output full internal representation of analysis result for sharing without need for recomputation
#22
corneliusroemer
opened
2 years ago
2
Have a look at the Δm, n, 2 statistic for breakpoint detection
#21
lenaschimmel
opened
2 years ago
0
Add relevant primer bed files and make sure the bed format is correctly interpreted
#20
lenaschimmel
opened
2 years ago
0
ENH: provide output optionally as csv/tsv for automated analysis/sharing
#19
corneliusroemer
closed
2 years ago
28
ENH: repeat gene legend every say 30 samples in case of long list
#18
corneliusroemer
opened
2 years ago
2
ENH: add spaces between genes rather than every 5 mutations
#17
corneliusroemer
opened
2 years ago
1
ENH: show progress bar, say how many files were read in, how processing is going
#16
corneliusroemer
closed
2 years ago
2
ENH: Differentiate between clade defining mutations and optional mutations
#15
corneliusroemer
opened
2 years ago
3
Q: Why show all donors not just the relevant ones?
#14
corneliusroemer
closed
2 years ago
6
ENH: Allow tool to run in a web browser
#13
corneliusroemer
opened
2 years ago
4
Allow more file formats and/or access methods, i.e. Auspice v2 dataset JSON from nextstrain URLs
#12
lenaschimmel
opened
2 years ago
0
Write documentation on how to interpret the output
#11
lenaschimmel
opened
2 years ago
0
Fix or remove 21I and 21J
#10
lenaschimmel
opened
2 years ago
11
Way to pipe results to png, txt files
#9
ghost
closed
2 years ago
7
Deltacrons with NSP3 breakpoint
#8
ktmeaton
opened
2 years ago
17
TypeError: unsupported operand type(s) for |: 'dict' and 'dict'
#7
arodzh-sudo
closed
2 years ago
1
Python version requirement 3.9
#6
benkraj
closed
2 years ago
2
Release a version
#5
erinyoung
opened
2 years ago
5
Find and use better source for typical mutations of lineages
#4
lenaschimmel
closed
2 years ago
14
Make tool pip-installable
#3
corneliusroemer
closed
2 years ago
4
Issues with VT / ANSI color codes, especially on Windows/Ubuntu
#2
lenaschimmel
opened
2 years ago
1
Update README.md
#1
tsymalla
closed
2 years ago
1