riboviz/riboviz

Issues

• Maize genome in riboviz format

  #485 opened a month ago by NastiaSkuba
  7

• Add sequence length divisible by 3 check to `check_fasta_gff.py`

  #484 opened 8 months ago by acope3
  0

• generateStatsFigs terminating when running vignettes

  #483 opened a year ago by hector3500
  1

• Assign parameters to processes in prep-riboviz-config.md

  #482 opened a year ago by ewallace
  0

• Problems with the Rlibrary in the Wallace group space

  #473 opened 2 years ago by Eldonoho99
  1

• Issue with `rhdf5::h5writeAttribute.integer` in `bam_to_h5_functions.R`

  #477 opened a year ago by acope3
  1

• Fix errors in bam_to_h5.R

  #479 opened a year ago by ewallace
  2

• Display figshare doi

  #478 opened 2 years ago by ewallace
  0

• generateStatsFigs on human ribose data is taking too long and then terminated with an error "Error in 2:end_reads_pos_subset : argument of length 0"

  #472 opened 2 years ago by Pradeep-ICR
  25

• Make collateTPMS code flexible to collate other variables

  #475 opened 2 years ago by ewallace
  0

• Hisat2 and Bowtie installation issue. Nextflow example issue.

  #474 opened 2 years ago by misaalbedi
  2

• Analysing Inhibitory Codon Pairs (ICP) for new species

  #468 opened 2 years ago by Eldonoho99
  24

• Refactor codon pairs scripts

  #436 opened 3 years ago by mikej888
  40

• Edit the code in codon_feature_analysis.R to give the whole window size not only position 0

  #470 opened 2 years ago by Eldonoho99
  11

• Ensure CDS features only are used in Codon (pair) counting

  #469 opened 2 years ago by ewallace
  1

• Upgrade Nextflow version to enable dsl1 flag

  #467 opened 2 years ago by Maberuiz
  1

• Flag for nextflow dsl 1

  #466 opened 2 years ago by ewallace
  5

• Upgrade Eddie documentation, 2022 edition

  #460 opened 2 years ago by ewallace
  7

• Executable permissions issue on Eddie cluster affecting riboviz repo

  #444 opened 2 years ago by FlicAnderson
  7

• Write contributor guide

  #459 opened 2 years ago by ewallace
  1

• Explore use of SRA functionality within HPC environments

  #441 opened 3 years ago by mikej888
  1

• "unable to initialize nextflow environment" issue on Eddie

  #455 opened 3 years ago by asnewell
  4

• Upgrade riboviz output files and figures documentation,2022 edition

  #465 opened 2 years ago by Eldonoho99
  0

• document num_processes better

  #464 opened 2 years ago by ewallace
  1

• Fix test documentation

  #461 opened 2 years ago by ewallace
  1

• h5ls does not give a full list of gene names

  #458 opened 2 years ago by acope3
  0

• Investigate test_bam_to_h5.R and test_bam_to_h5_functions.R warnings for rhdf 2.34.0

  #412 opened 3 years ago by mikej888
  2

• Point install page to container instructions

  #457 opened 3 years ago by ewallace
  0

• Using riboviz on Amarel

  #453 opened 3 years ago by acope3
  6

• Update developer documentation

  #443 opened 3 years ago by mikej888
  6

• Add documentation on how to develop further integration tests

  #435 opened 3 years ago by FlicAnderson
  5

• More on Eddie

  #414 opened 3 years ago by ewallace
  0

• Document how downloading results and moving them around may affect the shiny visualizations

  #430 opened 3 years ago by kavousan
  2

• Clarify that config file parameters override hard-coded parameters.

  #449 opened 3 years ago by ewallace
  1

• Change RiboViz to riboviz

  #421 opened 3 years ago by mikej888
  1

• Clarify naming convention for UTRs

  #451 opened 3 years ago by IsabelBirds
  2

• Document effect of hisat2 `-k` and `--non-deterministic` parameters

  #448 opened 3 years ago by mikej888
  0

• Update integration tests to better handle optional output files

  #418 opened 3 years ago by mikej888
  2

• Count reads only on CDS, in addition to on whole transcript?

  #413 opened 3 years ago by ewallace
  2

• Fix bug in `prep_riboviz.nf` `interactive_viz_params` construction

  #438 opened 3 years ago by mikej888
  1

• Fix file name bug in `run_shiny_server.R`

  #439 opened 3 years ago by mikej888
  1

• Test & add port forwarding documentation for interactive visualization

  #431 opened 3 years ago by FlicAnderson
  1

• Update file names in documentation and code

  #411 opened 3 years ago by 3mma-mack
  25

• Update documentation of ribogrid data by position and length to riboviz_outputs.md

  #426 opened 3 years ago by ewallace
  7

• Address outstanding usability issues in interactive visualization

  #433 opened 3 years ago by FlicAnderson
  2

• Check R code to replace all uses of gather() & spread() functions with pivot_*() equivalents

  #415 opened 3 years ago by FlicAnderson
  1

• Downloading results and moving them around may affect the shiny visualizations

  #410 opened 3 years ago by JOl-lN
  8

• Deprecate or document rpf parameter

  #429 opened 3 years ago by mikej888
  0

• Outputting a file that indicates the periodicity of reads of different length.

  #427 opened 3 years ago by ewallace
  0

• Workflow does not complete if `count_reads` is `true` but `run_static_html` is `false`

  #416 opened 3 years ago by mikej888
  7