xryanglab/RiboCode issues and pull requests

#64 - metaplot import error Python 3.10

Issue - State: open - Opened by ericmalekos 5 months ago

#63 - Question on handling multimappers

Issue - State: open - Opened by mosi223 7 months ago - 1 comment

#62 - No obviously periodicity are detected from bam file when running metaplots step

Issue - State: open - Opened by DooYal 8 months ago - 3 comments

#61 - No R script supp

Issue - State: open - Opened by rabc9 9 months ago

#60 - 请问如何进行lncRNA的ORF鉴定

Issue - State: closed - Opened by DooYal 10 months ago - 2 comments

#59 - Incorrect handling of hdf5 file for repeated runs of RiboCode

Issue - State: open - Opened by jdcla 12 months ago

#58 - RiboCode nf-core module

Issue - State: open - Opened by JackCurragh about 1 year ago

#57 - h5py TypeError: No conversion path for dtype: dtype('<U18')

Issue - State: open - Opened by huipan1973 over 1 year ago

#56 - Error, the references in bam are different from transcriptome annotation

Issue - State: closed - Opened by KONeill872 over 1 year ago

#55 - psites_number table is not generated with v1.2.15

Issue - State: open - Opened by hsinyenwu over 1 year ago - 1 comment

#54 - ValueError: unsupported pickle protocol: 5 in metaplots

Issue - State: open - Opened by z626093820 over 1 year ago - 1 comment

#53 - ModuleNotFoundError: No module named 'fasta'

Issue - State: open - Opened by fulaibaowang over 1 year ago - 6 comments

#52 - different transcripts of one gene

Issue - State: open - Opened by yx-xu about 2 years ago

#51 - Question on adjusted P values reported in collapsed output

Issue - State: open - Opened by mt1022 over 2 years ago - 2 comments

#50 - update to 1.2.15

Pull Request - State: closed - Opened by zhengtaoxiao over 2 years ago

#49 - Update metaplots.py

Pull Request - State: closed - Opened by zhengtaoxiao over 2 years ago

#48 - TypeError: '<' not supported between instances of 'str' and 'NoneType'

Issue - State: closed - Opened by LiTing99-cutie over 2 years ago - 2 comments

#47 - remove PCR duplicate

Issue - State: open - Opened by yx-xu over 2 years ago - 2 comments

#46 - Empty "transcripts_cds.txt" file

Issue - State: open - Opened by huguanjing over 2 years ago - 1 comment

#45 - 请问关于ORF预测结果中‘Psites_frame0_RPKM’代表什么意思？

Issue - State: open - Opened by z626093820 over 2 years ago - 4 comments

#44 - fix an error for ribocode_onestep

Pull Request - State: closed - Opened by zhengtaoxiao over 2 years ago

#43 - error in metaplots step

Issue - State: open - Opened by hugch2020 over 2 years ago - 1 comment

#42 - Whether multiple mapping affect ribocode result

Issue - State: open - Opened by Hilarialy over 2 years ago - 1 comment

#41 - RiboCode_onestep crashes when calling detectORF

Issue - State: open - Opened by trum994 over 2 years ago - 1 comment

#40 - can't locate attribute: psites_number

Issue - State: open - Opened by trum994 over 2 years ago - 1 comment

#39 - 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

Issue - State: closed - Opened by z626093820 over 2 years ago - 1 comment

#38 - plot_orf_density error,it show the following arguments are required: --start-codon

Issue - State: closed - Opened by z626093820 over 2 years ago

#37 - 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)

Issue - State: open - Opened by z626093820 over 2 years ago - 1 comment

#36 - Read counts issues

Issue - State: open - Opened by tan5251 over 2 years ago - 2 comments

#35 - ValueError: Can't transform the genomic interval, please check!

Issue - State: open - Opened by z626093820 over 2 years ago - 1 comment

#34 - Update to v1.2.14

Pull Request - State: closed - Opened by zhengtaoxiao over 2 years ago

#33 - prepare_transcripts not taking multiple CDSs into account

Issue - State: closed - Opened by Eduardo-vsouza almost 3 years ago - 1 comment

#32 - psites HDF5 file fails to be created

Issue - State: closed - Opened by Roleren almost 3 years ago - 1 comment

#31 - psite HDF5 file is saved in the wrong location

Issue - State: open - Opened by Roleren almost 3 years ago - 2 comments

#30 - Error in GTFupdate

Issue - State: open - Opened by lbwfff about 3 years ago - 1 comment

#29 - update plot_orf_density

Pull Request - State: closed - Opened by sherkinglee about 3 years ago

#28 - modify plot_orf_density function: add --ORF-type and --start--codon p…

Pull Request - State: closed - Opened by sherkinglee about 3 years ago - 2 comments

#27 - Change readme from pip to pip3

Issue - State: closed - Opened by Roleren over 3 years ago - 1 comment

#26 - error in GTFupdate

Issue - State: closed - Opened by L1angyan over 3 years ago

#25 - Alternative Start Codons

Issue - State: open - Opened by qidi-yang over 4 years ago - 1 comment

#24 - Update README.rst

Pull Request - State: closed - Opened by zhengtaoxiao almost 5 years ago

#23 - Detect C-terminal extensions with RiboCode

Issue - State: open - Opened by marcasriv almost 5 years ago

#22 - Error in <Preparing the transcripts annotation files> step

Issue - State: closed - Opened by yuechaowu about 5 years ago - 1 comment

#21 - GTF specification should include start and stop codons

Issue - State: open - Opened by ewallace about 5 years ago - 1 comment

#20 - Error when writing transcripts to file

Issue - State: open - Opened by ewallace about 5 years ago - 1 comment

#19 - Highlight the issue about GTF file

Pull Request - State: closed - Opened by zhengtaoxiao over 5 years ago

#18 - KeyError while reading BAM

Issue - State: closed - Opened by boboppie over 5 years ago - 2 comments

#17 - update to a new version

Pull Request - State: closed - Opened by zhengtaoxiao almost 6 years ago

#16 - Update the parsing_attr function

Pull Request - State: closed - Opened by zhengtaoxiao almost 6 years ago

#15 - Error in 'RiboCode'

Issue - State: closed - Opened by PSSUN almost 6 years ago - 4 comments

#14 - Error in 'prepare_transcripts'

Issue - State: closed - Opened by PSSUN almost 6 years ago - 1 comment

#13 - support py2 and py3

Pull Request - State: closed - Opened by zhengtaoxiao almost 6 years ago

#12 - small changes

Pull Request - State: closed - Opened by zhengtaoxiao about 6 years ago

#11 - small change of plot function

Pull Request - State: closed - Opened by zhengtaoxiao about 6 years ago

#10 - Unknown Attribute Error

Issue - State: closed - Opened by brendanwee about 6 years ago - 1 comment