rnabioco/raer

Issues

• Cannot open URL 'https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_000001405.40_GRCh38.p14/GCF_000001405.40_GRCh38.p14_assembly_report.txt'

  #121 opened 3 months ago by shmmuzhangh
  3

• provide diagram of data processing workflow

  #53 opened 3 months ago by kriemo
  4

• Cannot connect to ExperimentHub server

  #120 opened 3 months ago by shmmuzhangh
  5

• add support for DNAString/DNAstringSet

  #117 opened 7 months ago by kriemo
  0

• create gh release matching bioc version

  #114 opened a year ago by jayhesselberth
  0

• pkgdown error

  #104 opened a year ago by kriemo
  2

• handle false positive warning when expanding ranges

  #111 opened a year ago by kriemo
  0

• update vignette to use raerdata package

  #98 opened a year ago by kriemo
  0

• update vignette for new single-cell workflow

  #80 opened a year ago by jayhesselberth
  1

• functionality to examine expression of editing enzymes

  #82 opened a year ago by jayhesselberth
  1

• Create new GR annotation data for examples

  #77 opened a year ago by jayhesselberth
  0

• Increase size of sample data

  #73 opened a year ago by jayhesselberth
  2

• implement calc_AEI method for droplet scRNA-seq data

  #97 opened a year ago by kriemo
  0

• organizing databases and data resources

  #11 opened a year ago by kriemo
  6

• rename main to devel

  #88 opened a year ago by kriemo
  1

• GR output columns

  #59 opened 2 years ago by jayhesselberth
  1

• ref and alt naming of GR input for pileup_cells

  #84 opened 2 years ago by kriemo
  0

• option to exclude reporting low frequency multiallelics

  #72 opened 2 years ago by kriemo
  0

• add progress bar for get_pileup()

  #49 opened 2 years ago by jayhesselberth
  2

• feedback from filter functions

  #67 opened 2 years ago by jayhesselberth
  0

• don't export `count_edits`

  #75 opened 2 years ago by jayhesselberth
  0

• use RcppEigen

  #51 opened 2 years ago by jayhesselberth
  0

• additional analysis for main vignette

  #50 opened 2 years ago by jayhesselberth
  0

• Add notes on how to get to BAM

  #44 opened 2 years ago by jayhesselberth
  0

• speed up `remove_multiallelic()`?

  #60 opened 2 years ago by jayhesselberth
  1

• internal function for specialized bam sort

  #56 opened 2 years ago by jayhesselberth
  3

• report # of reads excluded from positions

  #27 opened 2 years ago by kriemo
  0

• add readme showing main functionality

  #8 opened 2 years ago by kriemo
  0

• just use native C rather than Rcpp

  #6 opened 2 years ago by kriemo
  1

• single cell processing workflow

  #4 opened 2 years ago by kriemo
  3

• pkgdown build

  #43 opened 2 years ago by jayhesselberth
  0

• reorganize source code

  #5 opened 2 years ago by kriemo
  0

• licensing and attributions

  #7 opened 2 years ago by kriemo
  1

• make vignette

  #3 opened 2 years ago by kriemo
  1

• Tests to check get_pileup calculations

  #15 opened 2 years ago by sheridar
  0

• check compatibilty with older rhtslib

  #36 opened 2 years ago by kriemo
  1

• windows build

  #13 opened 2 years ago by kriemo
  3

• add options to filter for specific variants in pileup

  #26 opened 2 years ago by kriemo
  0

• bulk rna-seq processing approach

  #10 opened 2 years ago by kriemo
  1

• Find condition specific changes

  #20 opened 2 years ago by kwells4
  1

• use only UMIs not all reads for single cell data

  #19 opened 3 years ago by kriemo
  2

• nRef and nVar stranded calculations

  #14 opened 3 years ago by sheridar
  2

• get_pileup width calculation

  #23 opened 3 years ago by sheridar
  1

• RangedSummarizedExperiment

  #9 opened 3 years ago by kriemo
  3

• devtools build utilities issue load_all and check error

  #12 opened 3 years ago by kriemo
  1

• tiny test data

  #2 opened 3 years ago by kriemo
  0

• better name

  #1 opened 3 years ago by kriemo
  1