Bioconductor/Biostrings

Issues

• consensusString and consensusMatrix error for legth-0 input

  #101 opened a year ago by jan-glx
  1

• Error when trying to convert string to DNAString

  #57 opened 5 months ago by evanpk
  1

• Encoding ASCII up to 255

  #65 opened 3 years ago by gevro
  13

• How can I color labels of phylogenetic tree generated with plot.phylo (Biostrings) by a dataframe value and add a color legend?

  #94 opened 7 months ago by segarka
  1

• get Seq off limits

  #100 opened 7 months ago by MelinaKlostermann
  2

• Sequence indcies out of bound when using matchPattern.

  #102 opened 7 months ago by Dan-Lt
  1

• AAString does not convert strings to upper case

  #84 opened 8 months ago by stitam
  1

• trimLRPatterns with indels not trimming as intended in case of net insertions or deletions between subject and pattern?

  #88 opened 2 years ago by jan-glx
  2

• alignedPattern and @pattern have different returns

  #92 opened 8 months ago by Close-your-eyes
  1

• Unnecessary warning when using `readQualityScaledDNAStringSet`

  #106 opened 10 months ago by LTLA
  0

• Error in reading fastq files

  #104 opened a year ago by apcristi
  4

• readDNAStringSet for fasta with long headers

  #59 opened a year ago by evaegelyng
  8

• NEWS/CHANGES: Not updated in 13+/9+ years

  #67 opened a year ago by HenrikBengtsson
  1

• Storing list of phredquality in a data.frame/table

  #105 opened a year ago by gevro
  4

• segfault error when saving Biostrings output

  #103 opened a year ago by gevro
  2

• loading "tictoc" package makes the object lost and cannot assign again

  #99 opened 2 years ago by qifei9
  5

• Amino Acid sequence to letter function

  #93 opened 2 years ago by LiNk-NY
  7

• matchPattern wildcard for AAstringset

  #34 opened 5 years ago by swuyts
  3

• Value of SET_STRING_ELT() must be a 'CHARSXP' not a 'raw'

  #95 opened 2 years ago by gevro
  4

• Error in .Call2("new_XStringSet_from_CHARACTER", class(x0), elementType(x0), : key 51 (char '3') not in lookup table

  #35 opened 5 years ago by heleendelbeke
  12

• confused about reading in a single long fasta subject sequence for pattern matching

  #89 opened 2 years ago by tchrisboles
  4

• adding single element to existing DNAStringSetList

  #39 opened 2 years ago by jayoung
  3

• Suggestion for Biostrings::translate - option to disambiguate

  #55 opened 2 years ago by ammaraziz
  1

• Is there any way to extract a sequence between two other sequences and allow for mismatches

  #56 opened 2 years ago by loukesio
  1

• Ns in DNAstringset greys out all text in console that follows

  #54 opened 2 years ago by proychou
  4

• Bug: AlignedSubject/AlignedPattern very slow

  #79 opened 2 years ago by gevro
  1

• Biostrings/vignettes/MultipleAlignments.Rnw

  #85 opened 2 years ago by jwokaty
  0

• vmatchpattern() with max.mismatch= 1 gives less results than with max.mismatch =0

  #69 opened 2 years ago by LN-rich
  4

• pairwiseAlignment: documentation question

  #81 opened 2 years ago by gevro
  4

• Missing documentation for compareStrings

  #80 opened 2 years ago by gevro
  2

• Bug: length of PairwiseAlignments

  #78 opened 2 years ago by gevro
  2

• bug (?) in DNAStringSetList element reassignment

  #75 opened 2 years ago by jayoung
  2

• S.h seems to be deprecated

  #66 opened 3 years ago by tillea
  7

• Error in .Call2("new_XStringSet_from_CHARACTER", class(x0), elementType(x0), : key 50 (char '2') not in lookup table

  #68 opened 3 years ago by safiqu
  1

• writeXStringSet on QualityScaledDNAStringSet should automatically set qualities=

  #43 opened 3 years ago by LTLA
  4

• Package installation fails in latest R 4.2.0-nightly

  #64 opened 3 years ago by mtiberti
  1

• narrow(x, start=, end=) does not trim quality information

  #62 opened 3 years ago by thallinger
  2

• DNAStringSet(x, start=, end=) loses quality information

  #61 opened 3 years ago by thallinger
  3

• readAxt() and DNAStringSet() are unable to keep lowercase sequences

  #63 opened 3 years ago by Abrar2652
  1

• replaceAt with VCF Object

  #60 opened 3 years ago by DarioS
  4

• from txdb/getSeq to fasta

  #58 opened 3 years ago by madzafv
  4

• trinucleotideFrequency Segmentation Fault if Input Data is Large

  #52 opened 3 years ago by DarioS
  3

• extract the "start" position of "matchPattern"

  #53 opened 3 years ago by jielab
  1

• Comparing single base DNAString with single character causes stack error

  #51 opened 3 years ago by Shians
  0

• Key error from new_XStringSet_from_CHARACTER call

  #47 opened 4 years ago by morien
  2

• Error with complement()

  #48 opened 4 years ago by didillysquat
  3

• Introduce checks for R interrupts in the C code?

  #45 opened 4 years ago by twmccart
  4

• FastqQuality as.matrix is overly complicated

  #38 opened 4 years ago by Andreas-Bio
  1

• readDNAStringSet fails with Legacy Mac (CR) line breaks

  #37 opened 4 years ago by FabianRoger
  2

• writeQualityScaledXStringSet omitted the third line

  #36 opened 4 years ago by wydty
  1