vanheeringen-lab/genomepy

Issues

• Add proxy support

  #246 opened 4 months ago by Mitmischer
  0

• Genomepy install gets stuck

  #245 opened 6 months ago by DavideBrex
  0

• does not load gtf with chromose information

  #244 opened 10 months ago by antonkulaga
  1

• search command fails with KeyError: 'submitter'

  #243 opened a year ago by papanikos
  3

• Logger config overrides client logger config

  #238 opened a year ago by uniqueg
  6

• Is the code complexity for code to strict?

  #135 opened a year ago by simonvh
  4

• index older versions of ensembl

  #151 opened a year ago by siebrenf
  0

• -p localfile

  #215 opened a year ago by davidhoover
  6

• please, allow to fix the version of ensembl!

  #224 opened a year ago by antonkulaga
  5

• URL Not Found for Rest Server

  #232 opened a year ago by Kekananen
  1

• certificate error when downloading an ensembl plant genome with annotations

  #233 opened a year ago by splaisan
  4

• UCSC MySQL mirror selection

  #239 opened a year ago by gokceneraslan
  6

• Partial matching for NCBI taxonomy identifiers is not great for automating genome retrieval

  #235 opened a year ago by uniqueg
  1

• Annotation files not set after fetching

  #237 opened a year ago by uniqueg
  2

• Option to maintain provider cache?

  #230 opened a year ago by bricoletc
  5

• instead of throwing gtfToGenePred errors it should tell user that they should be installed, otherwise users will think annotation download is broken

  #225 opened a year ago by antonkulaga
  2

• MySQL connection error

  #226 opened 2 years ago by oriolfornes
  1

• cannot install genomepy with conda on arm64 Mac OS X

  #221 opened 2 years ago by ctb
  2

• Issue with gtfToGenePred

  #217 opened 2 years ago by simonvh
  1

• genomepy fails when downloading from UCSC

  #213 opened 2 years ago by paumarc
  2

• Feature request: genome sizes

  #206 opened 2 years ago by bricoletc
  3

• Mitochondrial genome

  #203 opened 2 years ago by elichter
  1

• Caches are not thread-safe

  #130 opened 2 years ago by siebrenf
  0

• caching

  #164 opened 2 years ago by siebrenf
  4

• ensemblgenomes database borked

  #205 opened 2 years ago by siebrenf
  0

• issue with annotation in 0.12.0

  #202 opened 2 years ago by simonvh
  2

• details of external databases

  #200 opened 2 years ago by zhichengwang59
  1

• exactly matching NCBI assembly reports

  #187 opened 3 years ago by siebrenf
  0

• local provider

  #144 opened 3 years ago by siebrenf
  0

• Network Error

  #192 opened 3 years ago by ChaoXu1997
  1

• Using Rich for better terminal output

  #189 opened 3 years ago by Mr-Milk
  1

• How to get Dbxref=GeneID:100287102

  #179 opened 3 years ago by schmucr1
  4

• Error: no exon in id-IGHV3-64D-2 contains CDS 555851-556197

  #178 opened 3 years ago by schmucr1
  2

• genomepy install error

  #153 opened 3 years ago by fgualdr
  6

• Filter sequences in the annotation file

  #154 opened 3 years ago by jma1991
  2

• FR genomepy version in readme

  #166 opened 3 years ago by Maarten-vd-Sande
  2

• Mapping locations (develop branch) doesn't seem to work

  #163 opened 3 years ago by simonvh
  2

• Add a citation file.

  #177 opened 3 years ago by simonvh
  0

• DtypeWarning

  #176 opened 3 years ago by siebrenf
  0

• Import of `as_seqdict`

  #172 opened 3 years ago by simonvh
  9

• I broke Ensembl

  #149 opened 3 years ago by siebrenf
  0

• Progress bars?

  #138 opened 3 years ago by laserson
  1

• TemporaryDirectory unable to remove tmp dir on NTFS formated disk

  #142 opened 3 years ago by peterch405
  3

• chromosome order

  #146 opened 3 years ago by Phlya
  10

• Multiple genomes option?

  #145 opened 4 years ago by Ahmed-Shibl
  1

• bad filing on Ensembl

  #123 opened 4 years ago by siebrenf
  1

• gracefully test if provider is up

  #114 opened 4 years ago by siebrenf
  0

• Container Image (Docker/Singularity)???

  #119 opened 4 years ago by YogiOnBioinformatics
  6

• Genome.sizes dict contains str instead of int

  #110 opened 4 years ago by simonvh
  1

• genomepy install from url with error

  #113 opened 4 years ago by wangmhan
  2