xryanglab RiboCode issues

xryanglab / RiboCode

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MIT License

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issues

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pvalue cutoff changes the predicted p-site, which is detected at site that is not the peak in metplot function

#65 dougbarrows opened 2 months ago
0
metaplot import error Python 3.10

#64 ericmalekos opened 5 months ago
0
Question on handling multimappers

#63 mosi223 opened 7 months ago
1
No obviously periodicity are detected from bam file when running metaplots step

#62 DooYal opened 8 months ago
3
No R script supp

#61 rabc9 opened 9 months ago
0
请问如何进行lncRNA的ORF鉴定

#60 DooYal closed 8 months ago
2
Incorrect handling of hdf5 file for repeated runs of RiboCode

#59 jdcla opened 12 months ago
0
RiboCode nf-core module

#58 JackCurragh opened 1 year ago
0
h5py TypeError: No conversion path for dtype: dtype('<U18')

#57 huipan1973 opened 1 year ago
0
Error, the references in bam are different from transcriptome annotation

#56 KONeill872 closed 1 year ago
0
psites_number table is not generated with v1.2.15

#55 hsinyenwu opened 1 year ago
1
ValueError: unsupported pickle protocol: 5 in metaplots

#54 z626093820 opened 1 year ago
1
ModuleNotFoundError: No module named 'fasta'

#53 fulaibaowang opened 1 year ago
6
different transcripts of one gene

#52 yx-xu opened 2 years ago
0
Question on adjusted P values reported in collapsed output

#51 mt1022 opened 2 years ago
2
update to 1.2.15

#50 zhengtaoxiao closed 2 years ago
0
Update metaplots.py

#49 zhengtaoxiao closed 2 years ago
0
TypeError: '<' not supported between instances of 'str' and 'NoneType'

#48 LiTing99-cutie closed 2 years ago
2
remove PCR duplicate

#47 yx-xu opened 2 years ago
2
Empty "transcripts_cds.txt" file

#46 huguanjing opened 2 years ago
1
请问关于ORF预测结果中‘Psites_frame0_RPKM’代表什么意思？

#45 z626093820 opened 2 years ago
4
fix an error for ribocode_onestep

#44 zhengtaoxiao closed 2 years ago
0
error in metaplots step

#43 hugch2020 opened 2 years ago
1
Whether multiple mapping affect ribocode result

#42 Hilarialy opened 2 years ago
1
RiboCode_onestep crashes when calling detectORF

#41 trum994 opened 2 years ago
1
can't locate attribute: psites_number

#40 trum994 opened 2 years ago
1
No obviously periodicity are detected from bam file, it could be due to poor quality sequencing. Please check the metagene plots and try again by lowering the value of frame0_percent

#39 z626093820 closed 2 years ago
1
plot_orf_density error,it show the following arguments are required: --start-codon

#38 z626093820 closed 2 years ago
0
ImportError: cannot import name 'PPoly' from partially initialized module 'scipy.interpolate' (most likely due to a circular import) (/home/zhai2/miniconda3/lib/python3.8/site-packages/scipy/interpolate/__init__.py)

#37 z626093820 opened 2 years ago
1
Read counts issues

#36 tan5251 opened 2 years ago
2
ValueError: Can't transform the genomic interval, please check!

#35 z626093820 opened 2 years ago
1
Update to v1.2.14

#34 zhengtaoxiao closed 2 years ago
0
prepare_transcripts not taking multiple CDSs into account

#33 Eduardo-vsouza closed 2 years ago
1
psites HDF5 file fails to be created

#32 Roleren closed 2 years ago
1
psite HDF5 file is saved in the wrong location

#31 Roleren opened 2 years ago
2
Error in GTFupdate

#30 lbwfff opened 3 years ago
1
update plot_orf_density

#29 sherkinglee closed 3 years ago
0
modify plot_orf_density function: add --ORF-type and --start--codon p…

#28 sherkinglee closed 3 years ago
2
Change readme from pip to pip3

#27 Roleren closed 2 years ago
1
error in GTFupdate

#26 L1angyan closed 3 years ago
0
Alternative Start Codons

#25 qidi-yang opened 4 years ago
1
Update README.rst

#24 zhengtaoxiao closed 4 years ago
0
Detect C-terminal extensions with RiboCode

#23 marcasriv opened 4 years ago
0
Error in <Preparing the transcripts annotation files> step

#22 yuechaowu closed 5 years ago
1
GTF specification should include start and stop codons

#21 ewallace opened 5 years ago
1
Error when writing transcripts to file

#20 ewallace opened 5 years ago
1
Highlight the issue about GTF file

#19 zhengtaoxiao closed 5 years ago
0
KeyError while reading BAM

#18 boboppie closed 5 years ago
2
update to a new version

#17 zhengtaoxiao closed 5 years ago
0
Update the parsing_attr function

#16 zhengtaoxiao closed 5 years ago
0