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tanghaibao
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jcvi
Python library to facilitate genome assembly, annotation, and comparative genomics
BSD 2-Clause "Simplified" License
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Switch to using genomepy as a dependency instead of SizesFile
#628
tanghaibao
opened
4 months ago
0
[Bug] Phytozome fetch invalid
#627
alpapan
closed
4 months ago
4
Paralogs
#626
romseg
opened
4 months ago
0
Minor formatting changes
#625
tanghaibao
closed
4 months ago
0
Add --noprune opt to retain small features in microsynteny plots.
#624
Adamtaranto
closed
4 months ago
0
Short features from "extra features" BED missing in microsynteny plot
#623
wu116
closed
4 months ago
6
jcvi.compara.catalog - 0 anchors issue
#622
erika-r-moore
closed
5 months ago
4
Karyotype "Error: some genes in blocks can't be found, please rerun after making sure that bed file agree with simple file."
#621
jmpolinski
opened
5 months ago
0
AttributeError: module 'matplotlib' has no attribute 'colormaps'
#620
tclin422
closed
5 months ago
2
Issue with using jcvi in google colab
#619
whisperingkahuna
opened
6 months ago
3
Update agp.py
#618
anonymousdouble
closed
6 months ago
0
WARNING Shade: None found in coordinates, skipping
#617
Simple53
closed
6 months ago
2
AttributeError: 'LayoutLine' object has no attribute 'color
#616
mixle18
opened
6 months ago
0
Genes plotted in the wrong position
#615
Tong-Chen
closed
6 months ago
2
What is the meaning of x-axis and y-axis? Does it represent the number of genes?
#614
wang7760
closed
7 months ago
2
Create the input file for MSTMap
#613
Marije179
opened
7 months ago
0
add customize x y for genelabelrotation 0; add --outputprefix for customized output
#612
Tong-Chen
closed
7 months ago
1
Send logger to stderr
#611
tanghaibao
closed
7 months ago
0
Add back genelabelrotation in Synteny
#610
tanghaibao
closed
7 months ago
0
ValueError when running "python -m jcvi.graphics.synteny"
#609
hungweichen0327
closed
7 months ago
2
set label/chr size in layout file;add genelabel rotation parameter (customize x and y for rotation with angle 0)
#608
Tong-Chen
closed
7 months ago
0
Allow blank lines in bed file
#607
Tong-Chen
closed
7 months ago
1
How genes in blocks files are connected with layout file in microsynteny plot?
#606
Tong-Chen
closed
7 months ago
5
Change --add_chr to --human_chr
#605
tanghaibao
closed
8 months ago
0
How to use genetic map (markers.csv) file to scafold a haplotype phased assembly from contig level to pseudochromosome level.
#604
ap1438
opened
8 months ago
5
lastal: I was installed here with multi-threading disabled
#603
MR-D-CJ
opened
8 months ago
1
Extra opts in gff.bed()
#602
tanghaibao
closed
9 months ago
0
How to generate a transparent collinear images
#601
shiyi-pan
closed
9 months ago
1
Add a module logger
#600
tanghaibao
closed
9 months ago
0
How to draw lines to the inside
#599
hushaoqiang
closed
3 weeks ago
5
add ignore zero anchor parameter for skip no matches in batch search
#598
Tong-Chen
closed
9 months ago
0
add ignore zero anchor parameter for skip no matches in batch search
#597
Tong-Chen
closed
9 months ago
0
ALLMAPS KeyError: 'CHR01_1133501'
#596
mixle18
closed
9 months ago
3
Problems with .anchors file results
#595
C-grapes
closed
9 months ago
2
RuntimeError
#594
asianjoelshin
closed
9 months ago
4
why same gene can appear in different synteny block?
#593
bucongfan
closed
10 months ago
4
Add actions cache
#592
tanghaibao
closed
10 months ago
0
Fix regression due to natsorted (thanks @cutykaka, #588)
#591
tanghaibao
closed
10 months ago
0
jcvi.assembly.allmaps path error
#590
faye-romero
closed
10 months ago
4
Use natsorted in graphics.chromosome (thanks @cutykaka, #588)
#589
tanghaibao
closed
10 months ago
0
Miscellaneous chromosome sorting
#588
cutykaka
closed
10 months ago
3
Error when trying to generate pdf plots of anchoring a genome to a genetic map
#587
hrpelg
closed
6 months ago
1
Error when I want to generate a pdf.
#586
Neo-xbx-00
closed
9 months ago
1
AttributeError: 'LayoutLine' object has no attribute 'color'
#585
YYsama11
closed
3 months ago
0
--iter=2 flag in jcvi.compara.synteny mcscan doesnot provide any additional regions !
#584
UpalabdhaD
opened
11 months ago
1
Issue with jcvi.compara.synfind : ValueError: not enough values to unpack (expected 2, got 0)
#583
UpalabdhaD
closed
11 months ago
2
Overlapping genes in block output
#582
mariamarinr
closed
11 months ago
7
parameters or thresholds were used for LAST filtering
#581
JianhaiChen
closed
7 months ago
1
jcvi - MCscan - multiple species
#580
kullrich
closed
12 months ago
1
IndexError: list index out of range
#579
Alalakikun
opened
1 year ago
4
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