xryanglab/RiboCode

Issues

• No obviously periodicity are detected from bam file when running metaplots step

  #62 opened 8 months ago by DooYal
  2

• psites_number table is not generated with v1.2.15

  #55 opened 2 years ago by hsinyenwu
  1

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

  #65 opened 3 months ago by dougbarrows
  0

• TypeError: '<' not supported between instances of 'str' and 'NoneType'

  #48 opened 2 years ago by LiTing99-cutie
  2

• ModuleNotFoundError: No module named 'fasta'

  #53 opened 2 years ago by fulaibaowang
  6

• Question on adjusted P values reported in collapsed output

  #51 opened 2 years ago by mt1022
  2

• 请问如何进行lncRNA的ORF鉴定

  #60 opened 8 months ago by DooYal
  2

• metaplot import error Python 3.10

  #64 opened 5 months ago by ericmalekos
  0

• Question on handling multimappers

  #63 opened 7 months ago by mosi223
  1

• No R script supp

  #61 opened 9 months ago by rabc9
  0

• Incorrect handling of hdf5 file for repeated runs of RiboCode

  #59 opened a year ago by jdcla
  0

• RiboCode nf-core module

  #58 opened a year ago by JackCurragh
  0

• h5py TypeError: No conversion path for dtype: dtype('<U18')

  #57 opened a year ago by huipan1973
  0

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

  #45 opened 2 years ago by z626093820
  4

• Error, the references in bam are different from transcriptome annotation

  #56 opened a year ago by KONeill872
  0

• psites HDF5 file fails to be created

  #32 opened 3 years ago by Roleren
  1

• ValueError: unsupported pickle protocol: 5 in metaplots

  #54 opened 2 years ago by z626093820
  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 opened 3 years ago by z626093820
  1

• different transcripts of one gene

  #52 opened 2 years ago by yx-xu
  0

• remove PCR duplicate

  #47 opened 2 years ago by yx-xu
  2

• Change readme from pip to pip3

  #27 opened 2 years ago by Roleren
  1

• Empty "transcripts_cds.txt" file

  #46 opened 2 years ago by huguanjing
  1

• Error in GTFupdate

  #30 opened 3 years ago by lbwfff
  1

• can't locate attribute: psites_number

  #40 opened 3 years ago by trum994
  1

• RiboCode_onestep crashes when calling detectORF

  #41 opened 3 years ago by trum994
  1

• error in metaplots step

  #43 opened 3 years ago by hugch2020
  1

• Whether multiple mapping affect ribocode result

  #42 opened 3 years ago by Hilarialy
  1

• 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 opened 3 years ago by z626093820
  1

• psite HDF5 file is saved in the wrong location

  #31 opened 3 years ago by Roleren
  2

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

  #38 opened 3 years ago by z626093820
  0

• Read counts issues

  #36 opened 3 years ago by tan5251
  2

• ValueError: Can't transform the genomic interval, please check!

  #35 opened 3 years ago by z626093820
  1

• prepare_transcripts not taking multiple CDSs into account

  #33 opened 3 years ago by Eduardo-vsouza
  1

• error in GTFupdate

  #26 opened 3 years ago by L1angyan
  0

• prepare_transcripts failed

  #9 opened 6 years ago by manishbiotechie
  3

• Alternative Start Codons

  #25 opened 5 years ago by qidi-yang
  1

• Detect C-terminal extensions with RiboCode

  #23 opened 5 years ago by marcasriv
  0

• Error in 'RiboCode'

  #15 opened 5 years ago by PSSUN
  4

• GTF specification should include start and stop codons

  #21 opened 5 years ago by ewallace
  1

• Error when writing transcripts to file

  #20 opened 5 years ago by ewallace
  1

• Error in <Preparing the transcripts annotation files> step

  #22 opened 5 years ago by yuechaowu
  1

• KeyError while reading BAM

  #18 opened 6 years ago by boboppie
  2

• Error in 'prepare_transcripts'

  #14 opened 6 years ago by PSSUN
  1

• Unknown Attribute Error

  #10 opened 6 years ago by brendanwee
  1

• pickle.load() AttributeError: 'module' object has no attribute 'Gene'

  #2 opened 7 years ago
  5

• ImportError: No module named Tkinter

  #3 opened 7 years ago by zhengtaoxiao
  2

• Generating figures with matplotlib when DISPLAY variable is undefined or invalid

  #1 opened 8 years ago by zhengtaoxiao
  0