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Commits on Feb 23, 2022

• revise pirna shortened names so highlighting works in expression plotting app

  

  Leah Kemp

  committed
  bff904a

• shorten piRNA names for plotting sakes

  

  Leah Kemp

  committed
  01ed13a

• fix

  

  Leah Kemp

  committed
  ff0d1f1

Commits on Feb 21, 2022

• update grabbing dataset and pipeline variables from dataset names

  

  Leah Kemp

  committed
  b7b26a3

• ensure datasets not analysed aren't analysed

  

  Leah Kemp

  committed
  3b0183f

• typo

  

  Leah Kemp

  committed
  5daf980

Commits on Feb 2, 2022

• tidy up

  

  Leah Kemp

  committed
  a3880f7

• fix

  

  Leah Kemp

  committed
  8ac7b90

• forgot to rename rds objects too

  

  Leah Kemp

  committed
  c5a48c9

Commits on Feb 1, 2022

• woops

  

  Leah Kemp

  committed
  a38f287

• fix typo

  

  Leah Kemp

  committed
  9d7820f

• remove any rows/RNA's with no counts found in any sample

  

  Leah Kemp

  committed
  12268aa

• rename rnas in prepare_counts.R so naming is consitant throught docs

  

  Leah Kemp

  committed
  3a78b3c

Commits on Jan 28, 2022

• use RDS objects to reduce duplicate compuation

  

  Leah Kemp

  committed
  f51fb4d

• also export log cpm as rds objects

  

  Leah Kemp

  committed
  aeb6ac5

Commits on Dec 16, 2021

• remove weird tRNA row from tRNA dataset

  

  Leah Kemp

  committed
  e38ac6d

Commits on Dec 5, 2021

• add export count datasets to rds objects

  

  Leah Kemp

  committed
  2e6ce10

Commits on Nov 30, 2021

• allow MDS of gencodes by having column in count dataset for which gencodes isn't split into diff rna species

  

  Leah Kemp

  committed
  cdf4d30

Commits on Nov 9, 2021

• use mirtop count data over edger count data for post-pipeline analyses

  

  Leah Kemp

  committed
  2fe2769

Commits on Nov 2, 2021

• change input fastq file naming convention to a more generic form

  

  Leah Kemp

  committed
  9657608

Commits on Oct 12, 2021

• add test pipeline outputs and several updates

  

  Leah Kemp

  committed
  e0c96eb

Commits on Oct 10, 2021

• overhaul incl. a single rmd to run all analyses in R

  

  Leah Kemp

  committed
  73a188c

Commits on Oct 5, 2021

• update depreciated functions

  

  Leah Kemp

  committed
  32c8dba

• update depreciated functions

  

  Leah Kemp

  committed
  c6f9d66

• pin down packages and fix

  

  Leah Kemp

  committed
  b8d510d

Commits on Sep 29, 2021

• add more stuff to config and update code to deal with this

  

  Leah Kemp

  committed
  115363c

Commits on Sep 28, 2021

• forgot to tidy smrnaseq sample names

  

  Leah Kemp

  committed
  5fc0ca6

• forgot to tidy smrnaseq sample names

  

  Leah Kemp

  committed
  0463d59

• updatepdate doc to use config

  

  Leah Kemp

  committed
  01f96f1

• updatepdate doc to use config

  

  Leah Kemp

  committed
  21b35db

Commits on Sep 27, 2021

• update

  

  Leah Kemp

  committed
  9ffeb97

• updates

  

  Leah Kemp

  committed
  fc17481

• fix + add more to counts processing

  

  Leah Kemp

  committed
  d51ec14

• update

  

  Leah Kemp

  committed
  05453d4

• add process counts doc

  

  Leah Kemp

  committed
  901947d

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