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Magdoll
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cDNA_Cupcake
Miscellaneous collection of Python and R scripts for processing Iso-Seq data
BSD 3-Clause Clear License
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collapse_isoforms_by_sam.py out of memory
#250
SY348
opened
5 months ago
0
cdna_cupcake与SQANTI3
#249
tky199996
opened
6 months ago
0
Demultiplex after clustering / genome alignment
#248
davidvilanova
opened
6 months ago
0
fusion_finder.py
#247
tky199996
opened
7 months ago
1
ModuleNotFoundError: No module named 'cupcake.tofu' after installing cdna_cupcake in conda subenv
#246
LilyLuyang
closed
6 months ago
3
AttributeError: module 'numpy' has no attribute 'int'.
#245
Journeyant
closed
6 months ago
2
Saturation analysis bug fixes; compatibility with newer isoseq cluster [make_file_for_subsampling_from_collapsed.py]
#244
mrendleman
opened
11 months ago
0
minor updates for python-3
#243
brianjohnhaas
closed
1 year ago
0
solved
#242
gengbaobao
opened
1 year ago
0
Cython compiler error when installing/building cDNA_cupcake
#241
skchronicles
opened
1 year ago
2
fusion_collate_info.py KeyError: 'count_fl'
#240
sonyuna90
closed
6 months ago
3
add language_level
#239
ChangqingW
opened
1 year ago
0
setup.py requires sklearn instead of scikit-learn
#238
cyrilcros
closed
1 year ago
1
run_preCluster.py
#237
jordur
closed
1 year ago
1
TypeError: iter_gmap_sam() got an unexpected keyword argument 'type' using collapse_isoforms_by_sam.py
#236
gyorkeia
opened
1 year ago
0
fusion_collate_info.py script has bugs and its not working.
#235
unique379r
opened
1 year ago
0
lima for skera.bam
#234
hmyh1202
opened
1 year ago
0
cluster id cleaned in get_abundance_post_collapse
#233
ssutharzan
closed
1 year ago
0
Create sam format for collapse_isoforms_by_sam.py
#232
rodrisenovilla
opened
2 years ago
0
cupcake2 directory missing, compilation fails
#231
dvargaslandin
opened
2 years ago
4
chain_samples.py does not work!
#230
unique379r
opened
2 years ago
0
cluster id mismatch issue in get_abundance_post_collapse.py
#229
ssutharzan
closed
1 year ago
3
Question: where does the count.txt file come from?
#228
mad-scientist-in-training
opened
2 years ago
0
Struggling in identifying the true positive fusion transcripts outputting from fusion_finder.py
#227
wzhang42
opened
2 years ago
0
How to configure the correct /optimal parameter and validate the true positive from PB fusion candidate list.
#226
wzhang42
opened
2 years ago
0
Forward link display 404
#225
wzhang42
closed
2 years ago
1
Where to find the demo data (input.fasta) used in fusion transcript finding (https://github.com/Magdoll/cDNA_Cupcake/wiki/Best-practice-for-fusion-transcript-finding)
#224
wzhang42
closed
2 years ago
2
demux_isoseq_with_genome.py Issue - expecting input not generated by get_abundance_post_collapse.py
#223
KrRi4
opened
2 years ago
0
pkg_resources.ResolutionError when running "collapse_isoforms_by_sam.py"
#220
ssaif-cellarity
opened
2 years ago
2
Error about demux_isoseq_with_genome.py
#219
Yuzhang0102
opened
2 years ago
0
collapse with some data was very slow
#209
shizhuoxing
opened
2 years ago
1
collapse_isoforms_by_sam.py giving me SyntaxError at multiple points
#200
philoel
closed
2 years ago
2
collapse_isoforms_by_sam.py - can not iterate over samfile without header
#199
ckitsoulis
opened
2 years ago
2
Calling variants using IsoPhase from Iso-Seq data
#198
Yexin-Zhang
opened
2 years ago
1
Parallel processing in subsample.py
#197
SichongP
opened
2 years ago
0
Fix seurat input script
#196
velociroger-pb
closed
2 years ago
0
Don't merge sample by chain_samples.py
#195
2209983424
opened
2 years ago
0
Is there a hard limit on inter-exonic ranges?
#194
markb729
opened
2 years ago
1
ISSUE: fusion_finder.py
#193
tay45
closed
2 years ago
1
chain_samples.py Exception: Sanity check failed!
#192
tabeariepe
opened
2 years ago
0
Error with sqanti3_qc.py, halting while executing SQANTI3_report.R
#191
sunnyd13579
closed
2 years ago
1
Get the fusion position of the fusion transcripts
#190
pailloufat-stack
closed
2 years ago
0
little typo
#189
splaisan
closed
2 years ago
1
error while trying to run collapse_isoforms_by_sam.py
#188
BeatrizdeToledo
closed
2 years ago
1
The question about finding fusion genes
#187
2209983424
closed
1 year ago
3
No out put with get_abundance_post_collapse.py
#186
B10inform
opened
2 years ago
7
collapse_isoforms_by_sam.py No module named 'cupcake.tofu.branch.c_branch'
#185
kechalar-hua
closed
2 years ago
1
Script 'scripts/collapse_isoforms_by_sam.py' not found in metadata at '/research/rgs01/home/clusterHome/xchen2/software/cDNA_Cupcake/cupcake.egg-info'
#184
xiaolongchen0627
closed
2 years ago
4
MTX appears to have the wrong number of entries
#183
nsalomonis
closed
2 years ago
2
Python version
#182
tay45
closed
2 years ago
2
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