thelovelab/tximport

Issues

• tximport of kallisto h5s generated with multiple threads is not deterministic

  #58 opened 7 months ago by ning-y
  1

• tximport of feature counts?

  #55 opened a year ago by marwa38
  1

• import using tximport for the rsem count table to get integers?

  #52 opened a year ago by marwa38
  3

• Different length and counts depending on the number of loaded samples

  #54 opened a year ago by FlorianRocher
  1

• Dealing with multispecies using tximport

  #53 opened a year ago by FlorianRocher
  4

• error in 1:nrow(m): argument of length 0

  #51 opened 2 years ago by SylwiaPiatkowska
  1

• Which measure to use for gene Fold change analysis between pre- and post-treatment samples and for gene comparison within a sample

  #49 opened 3 years ago by mpunta
  1

• `ignoreAfterBar` not used if `txOut=TRUE`

  #40 opened 4 years ago by csoneson
  5

• Tximport issue with new R version

  #47 opened 4 years ago by alexandregmartini
  2

• Read in files in parallel

  #46 opened 4 years ago by grst
  4

• Returns TPM when abundanceCol is set to any value for type='rsem'

  #44 opened 4 years ago by csmith-pact
  1

• Recomended count scaling method for DTU analysis

  #43 opened 4 years ago by kvittingseerup
  2

• Import processed data

  #42 opened 4 years ago by koenvandenberge
  3

• cann't import kallisto abundance.h5/.tsv

  #41 opened 5 years ago by Ci-TJ
  4

• Add option to import only whitelisted barcodes from alevin

  #37 opened 5 years ago by csoneson
  2

• lose transcript names for salmon inferential replicates

  #39 opened 5 years ago by cindywen96
  0

• ignoreAfterBar does not apply with txOut=T and countsFromAbundance != "no"

  #38 opened 5 years ago by karl616
  1

• Move Alevin import code to C++

  #35 opened 5 years ago by mikelove
  3

• Missing release tags

  #36 opened 5 years ago by smoe
  1

• Outdated vignette?

  #34 opened 5 years ago by TobiTekath
  1

• can't read alevin output from salmon 0.14.0

  #32 opened 5 years ago by alexvpickering
  8

• Error in importing RSEM gene level result files

  #33 opened 5 years ago by Duanzpwt
  0

• sparse matrix support?

  #25 opened 5 years ago by koenvandenberge
  22

• Error against the result of salmon with option --numBootstraps

  #31 opened 5 years ago by kokitsuyuzaki
  1

• Importing transcript abundance datasets generated with Salmon 0.14.0

  #29 opened 5 years ago by edoardobertolini
  5

• Error in H5Fopen

  #27 opened 6 years ago by uso2015
  1

• Transcript expression collapsing to gene-level expression

  #26 opened 6 years ago by beginner984
  3

• Idea: Supporting alevin output

  #24 opened 6 years ago by PeteHaitch
  10

• Feature Idea : Derive abundance from inferential replicates

  #23 opened 6 years ago by rob-p
  2

• filtering lowly expreed genes after or before normalization ?

  #22 opened 7 years ago by atasub
  1

• Check for existence of abundance.h5 before checking for rhdf5?

  #21 opened 7 years ago by csoneson
  1

• Enabling reading from cloud storage

  #20 opened 7 years ago by tomsing1
  3

• Please read this before submitting an issue or PR

  #19 opened 7 years ago by mikelove
  0

• work with cuffnorm collated files

  #3 opened 8 years ago by mikelove
  0

• make it easier to read in rsem tx-level ests

  #11 opened 8 years ago by mikelove
  1

• Error: all(file.exists(files)) is not TRUE

  #17 opened 8 years ago by cartal
  1

• Typo in instructions for using ensembldb

  #16 opened 8 years ago by PeteHaitch
  0

• Unexpected behavior when processing RSEM transcript level files

  #15 opened 9 years ago by ecoenen
  1

• Allow missing-ness in individual transcriptomes

  #14 opened 9 years ago by mdshw5
  2

• better warning if no tx2gene provided

  #10 opened 9 years ago by mikelove
  0

• feature request: modularize gene-level summarization when txOut=TRUE

  #12 opened 9 years ago by stephenturner
  2

• rename argument: gene2tx => tx2gene

  #13 opened 9 years ago by mikelove
  0

• effective length for salmon

  #1 opened 9 years ago by mikelove
  0

• more flexible file designation for sailfish

  #5 opened 9 years ago by stephenturner
  6

• update docs and/or code wrt sailfish support

  #2 opened 9 years ago by mikelove
  0

• salmon/sailfish importer rework

  #8 opened 9 years ago by mikelove
  1

• Move `DESeqDataSetFromTximport` into tximport for now?

  #7 opened 9 years ago by mdshw5
  2

• Error in 1:nrow(m): argument of length 0

  #4 opened 9 years ago by stephenturner
  3