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2020update #169

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Commits on Oct 26, 2017

  1. try rstudio folder 

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  2. update docker and its information 

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Commits on Oct 27, 2017

  1. fix sildist bug in SC3 

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  2. fix cluster installation 

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  3. add projection; fix M3Drop bug 

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  4. update index; switch off half of the chapters 

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  5. move snn-cliq and MAGIC to utils 

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  6. fix last chapters 

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  7. activate first chapters 

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  8. update README 

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  9. fix imputation, update chapter numbers 

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  10. add scfind 

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  11. update the course website 

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  12. update the course website 

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  13. polishing up to chapter 11 inclusive 

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  14. Update 21-imputation.Rmd 

    Updated links and minor changes

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  15. Merge branch 'master' of https://github.com/hemberg-lab/scRNA.seq.course 

    

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  16. Merge pull request #128 from hemberg-lab/mhemberg-patch-1 

    Update 21-imputation.Rmd

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  17. Merge branch 'master' of https://github.com/hemberg-lab/scRNA.seq.course 

    

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  18. update imputation 

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  19. update imputation 

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  20. update seurat 

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Commits on Oct 28, 2017

  1. add limma 

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  2. fix chapter 8 

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  3. update the course website 

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  4. update the course website 

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  5. update expression chapter; some minor updates 

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  6. Merge branch 'master' of https://github.com/hemberg-lab/scRNA.seq.course 

    

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  7. add ARI; minor updates 

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Commits on Oct 29, 2017

  1. update the course website 

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  2. activate pdf building again 

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  3. Merge branch 'master' of https://github.com/hemberg-lab/scRNA.seq.course 

    

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  4. update the course website 

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  5. update the course website 

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  6. update bib file with betterbib tool 

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  7. Merge branch 'master' of https://github.com/hemberg-lab/scRNA.seq.course 

    

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  8. update the course website 

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Commits on Oct 30, 2017

  1. Update 27-ideal-scrnaseq-pipeline.Rmd 

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  2. Merge branch 'tallulandrews-patch-1' 

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  3. minor text updates 

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  4. Fixed typos 

    Fixed typos

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  5. Merge branch 'master' of https://github.com/hemberg-lab/scRNA.seq.course 

    

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  6. Fixed typos 

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  7. Fixed text 

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  8. Fixed typos 

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  9. Minor fixes 

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  10. Fixed typo 

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  11. Minor changes 

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  12. Merge branch 'master' into mhemberg-patch-1 

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  13. Merge branch 'mhemberg-patch-1' 

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  14. Merge branch 'master' into mhemberg-patch-2 

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  15. Merge branch 'mhemberg-patch-2' 

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  16. Merge branch 'master' into mhemberg-patch-3 

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  17. Merge branch 'mhemberg-patch-3' 

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  18. Merge branch 'master' into mhemberg-patch-4 

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  19. Merge branch 'mhemberg-patch-4' 

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  20. Merge branch 'master' into mhemberg-patch-5 

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  21. Merge branch 'mhemberg-patch-5' 

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  22. final updates 

    Merge branch 'master' into mhemberg-patch-6

# Conflicts:
#	26-seurat.Rmd


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  23. Merge branch 'mhemberg-patch-6' 

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  24. update the course website 

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  25. switch off pdf building

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Commits on Oct 31, 2017

  1. update the course website

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Commits on Nov 1, 2017

  1. update the course website

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  2. Add exercise solutions

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Commits on Nov 2, 2017

  1. update index page

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  2. move to Bioconductor release branch

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  3. Merge branch 'master' of github.com:hemberg-lab/scRNA.seq.course

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Commits on Nov 6, 2017

  1. add RUVSeq dependency

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  2. trying to fix RMySQL

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Commits on Nov 7, 2017

  1. Fix dropout chapter

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  2. update the course website

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  3. update the course website

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Commits on Nov 8, 2017

  1. update the course website

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  1. update the course website

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  1. update the course website

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  1. update the course website

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  1. update the course website

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  1. update the course website

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  1. update the course website

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  1. update the course website

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  1. update the course website

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  1. update the course website

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  1. update the course website

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  1. update the course website

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  1. update the course website

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  1. update the course website

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Commits on Nov 24, 2017

  1. fix pseudotime chapter

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Commits on Dec 11, 2017

  1. Fix mnn_correct issues; update Youtube link on the main page

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Commits on Dec 13, 2017

  1. fix mnnCorrect problem for reads

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Commits on Dec 18, 2017

  1. switch off normalisatio by gene length (it's wrong and biomaRt call f… 

    …ails every now and then)
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Commits on Dec 19, 2017

  1. forgot to add eval=FALSE

    wikiselev committed Dec 19, 2017
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Commits on Jan 11, 2018

  1. Add Lab5 - download Tabula Muris 

    Attempts to use bash within Rmd file which according to the documentation available online should be possible.
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Commits on Jan 12, 2018

  1. First half of introduction to R lab

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  2. First half of introduction to R lab

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  3. Delete L3-intro-to-R.Rmd

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  4. Add colour explanation

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  5. Update L3-intro-to-R.Rmd

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Commits on Jan 14, 2018

  1. feature_symbol is requried in the newest version of SC3

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  2. Merge branch 'master' of github.com:hemberg-lab/scRNA.seq.course

    wikiselev committed Jan 14, 2018
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Commits on Jan 15, 2018

  1. First half of processing raw data lab

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Commits on Jan 16, 2018

  1. add mnnCorrect diagram

    @tallulandrews
    tallulandrews authored Jan 16, 2018
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  2. fix imputation and scmap

    wikiselev committed Jan 16, 2018
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  3. Update 24-projection.Rmd 

    Add mnnCorrect, Metaneighbour, CCA
    @tallulandrews
    tallulandrews authored Jan 16, 2018
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  4. CCA (Seurat) plots 

    Chapter does not actually run any Seurat to avoid the library errors.
    @tallulandrews
    tallulandrews authored Jan 16, 2018
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  5. New Cross-dataset diagrams

    @tallulandrews
    tallulandrews authored Jan 16, 2018
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  6. Update 24-projection.Rmd 

    update diagrams
    @tallulandrews
    tallulandrews authored Jan 16, 2018
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Commits on Jan 17, 2018

  1. update the course website

    @wikiselev
    wikiselev committed Jan 17, 2018
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  2. update the course website

    @wikiselev
    wikiselev committed Jan 17, 2018
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Commits on Jan 18, 2018

  1. JW first draft of reads QC lab 1

    jenni-westoby committed Jan 18, 2018
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  2. update the course website

    @wikiselev
    wikiselev committed Jan 18, 2018
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  3. JW added wget commands to download Kolod et al. data

    jenni-westoby committed Jan 18, 2018
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  4. JW first draft of alignment lab including images used in Rmd

    jenni-westoby committed Jan 18, 2018
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Commits on Jan 19, 2018

  1. update the course website

    @wikiselev
    wikiselev committed Jan 19, 2018
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Commits on Jan 20, 2018

  1. update the course website

    @wikiselev
    wikiselev committed Jan 20, 2018
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Commits on Jan 21, 2018

  1. update the course website

    @wikiselev
    wikiselev committed Jan 21, 2018
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  2. update Dockerfile, add processing software

    wikiselev committed Jan 21, 2018
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  3. Merge branch 'master' of github.com:hemberg-lab/scRNA.seq.course

    wikiselev committed Jan 21, 2018
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  4. add curl

    wikiselev committed Jan 21, 2018
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  5. fix R packages installation

    wikiselev committed Jan 21, 2018
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Commits on Jan 22, 2018

  1. add fastqc, kallisto, bedtools2 and cutadapt

    wikiselev committed Jan 22, 2018
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  2. update the course website

    @wikiselev
    wikiselev committed Jan 22, 2018
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Commits on Jan 23, 2018

  1. fix bedtools; remove unnessesary software

    wikiselev committed Jan 23, 2018
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  2. Merge branch 'master' of github.com:hemberg-lab/scRNA.seq.course

    wikiselev committed Jan 23, 2018
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  3. fix bedtools again

    wikiselev committed Jan 23, 2018
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  4. update the course website

    @wikiselev
    wikiselev committed Jan 23, 2018
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Commits on Jan 24, 2018

  1. fix kallisto; update README

    wikiselev committed Jan 24, 2018
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  2. Merge branch 'master' of github.com:hemberg-lab/scRNA.seq.course

    wikiselev committed Jan 24, 2018
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  3. update the course website

    @wikiselev
    wikiselev committed Jan 24, 2018
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Commits on Jan 25, 2018

  1. add tidyverse and ggfortify

    wikiselev committed Jan 25, 2018
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  2. Merge branch 'master' of github.com:hemberg-lab/scRNA.seq.course

    wikiselev committed Jan 25, 2018
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  3. Upload 2000 transcript transcriptome -JW

    jenni-westoby committed Jan 25, 2018
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  4. update the course website

    @wikiselev
    wikiselev committed Jan 25, 2018
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Commits on Jan 26, 2018

  1. All files checked against docker image except L4 - JW

    jenni-westoby committed Jan 26, 2018
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  2. update the course website

    @wikiselev
    wikiselev committed Jan 26, 2018
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Commits on Jan 27, 2018

  1. update the course website

    @wikiselev
    wikiselev committed Jan 27, 2018
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Commits on Jan 28, 2018

  1. Add demultiplexing lab

    @tallulandrews
    tallulandrews authored Jan 28, 2018
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  2. Update L3-intro-to-R.Rmd

    @tallulandrews
    tallulandrews authored Jan 28, 2018
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Commits on Jan 29, 2018

  1. demultiplexing example data

    @tallulandrews
    tallulandrews authored Jan 29, 2018
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  2. ID true cell barcodes example data

    @tallulandrews
    tallulandrews authored Jan 29, 2018
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Commits on Jan 30, 2018

  1. merge new chapters from devel branch 

    Merge branch 'devel'

# Conflicts:
#	24-projection.Rmd
    wikiselev committed Jan 30, 2018
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  2. update the course website

    @wikiselev
    wikiselev committed Jan 30, 2018
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Commits on Jan 31, 2018

  1. remove empty continuation lines

    wikiselev committed Jan 31, 2018
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  2. Merge branch 'master' of github.com:hemberg-lab/scRNA.seq.course

    wikiselev committed Jan 31, 2018
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  3. update the course website

    @wikiselev
    wikiselev committed Jan 31, 2018
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  4. order chapters

    wikiselev committed Jan 31, 2018
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  5. Merge branch 'master' of github.com:hemberg-lab/scRNA.seq.course

    wikiselev committed Jan 31, 2018
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Commits on Feb 1, 2018

  1. Update 05-L1-process-raw.Rmd 

    Requires "perl" installed. (any version should be fine).
    @tallulandrews
    tallulandrews authored Feb 1, 2018
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  2. Update 30-de-real.Rmd

    @tallulandrews
    tallulandrews authored Feb 1, 2018
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  3. install trim_galore; minor edits

    wikiselev committed Feb 1, 2018
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  4. Update 05-L1-process-raw.Rmd 

    add reference to all samtools .cram calls
    @tallulandrews
    tallulandrews authored Feb 1, 2018
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  5. update trim_galore link

    wikiselev committed Feb 1, 2018
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  6. Add demultiplexing perl scripts

    @tallulandrews
    tallulandrews authored Feb 1, 2018
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  7. Merge branch 'devel' of github.com:hemberg-lab/scRNA.seq.course into … 

    …devel
    wikiselev committed Feb 1, 2018
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  8. Merge branch 'devel' of github.com:hemberg-lab/scRNA.seq.course into … 

    …devel
    wikiselev committed Feb 1, 2018
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  9. Update 05-L1-process-raw.Rmd 

    Add random seed and fully tested.
    @tallulandrews
    tallulandrews authored Feb 1, 2018
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  10. Update 06-L1-process-raw-align.Rmd

    @tallulandrews
    tallulandrews authored Feb 1, 2018
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  11. Update 09-L3-intro-to-R.Rmd

    @tallulandrews
    tallulandrews authored Feb 1, 2018
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  12. Update 13-L5-Intro-TabulaMuris.Rmd 

    fix bug
    @tallulandrews
    tallulandrews authored Feb 1, 2018
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  13. split dockerfile in two

    wikiselev committed Feb 1, 2018
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  14. Merge branch 'devel' of github.com:hemberg-lab/scRNA.seq.course into … 

    …devel
    wikiselev committed Feb 1, 2018
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  15. Merge branch 'master' of github.com:hemberg-lab/scRNA.seq.course

    wikiselev committed Feb 1, 2018
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  16. update Dockerfile

    wikiselev committed Feb 1, 2018
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Commits on Feb 2, 2018

  1. remove less

    wikiselev committed Feb 2, 2018
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  2. Add metaneighbour

    @tallulandrews
    tallulandrews authored Feb 2, 2018
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  3. Update 31-projection.Rmd 

    Fix bugs
    @tallulandrews
    tallulandrews authored Feb 2, 2018
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  4. update the course website

    @wikiselev
    wikiselev committed Feb 2, 2018
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  5. Update 05-L1-process-raw.Rmd 

    Fix Formatting
    @tallulandrews
    tallulandrews authored Feb 2, 2018
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  6. Update 13-L5-Intro-TabulaMuris.Rmd 

    clean up output messages
    @tallulandrews
    tallulandrews authored Feb 2, 2018
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  7. Update 14-exprs-qc.Rmd

    @tallulandrews
    tallulandrews authored Feb 2, 2018
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  8. JW fixed references and tested code on AWS

    jenni-westoby committed Feb 2, 2018
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  9. JW fixed references and tested code on AWS

    jenni-westoby committed Feb 2, 2018
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  10. Merge branch 'devel' of https://github.com/hemberg-lab/scRNA.seq.course

    jenni-westoby committed Feb 2, 2018
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  11. Merge branch 'devel'

    wikiselev committed Feb 2, 2018
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  12. Merge branch 'devel'

    wikiselev committed Feb 2, 2018
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  13. update the course website

    @wikiselev
    wikiselev committed Feb 2, 2018
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  14. update the headers

    wikiselev committed Feb 2, 2018
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  15. update main page, clean the docs folder

    wikiselev committed Feb 2, 2018
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  16. update README; add empty-file to docs

    wikiselev committed Feb 2, 2018
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  17. remove year

    wikiselev committed Feb 2, 2018
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  18. update the course website

    @wikiselev
    wikiselev committed Feb 2, 2018
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  19. fix some outputs

    wikiselev committed Feb 2, 2018
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  20. Merge branch 'master' of github.com:hemberg-lab/scRNA.seq.course

    wikiselev committed Feb 2, 2018
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  21. update the course website

    @wikiselev
    wikiselev committed Feb 2, 2018
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Commits on Feb 3, 2018

  1. update the course website

    @wikiselev
    wikiselev committed Feb 3, 2018
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  2. hide projection chapter

    wikiselev committed Feb 3, 2018
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  3. Merge branch 'master' of github.com:hemberg-lab/scRNA.seq.course

    wikiselev committed Feb 3, 2018
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  4. update the course website

    @wikiselev
    wikiselev committed Feb 3, 2018
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Commits on Feb 4, 2018

  1. update the course website

    @wikiselev
    wikiselev committed Feb 4, 2018
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Commits on Feb 5, 2018

  1. Updating pseudotime chapter.

    @davismcc
    davismcc committed Feb 5, 2018
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  2. update the course website

    @wikiselev
    wikiselev committed Feb 5, 2018
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  3. Merge branch 'devel' of git://github.com/davismcc/scRNA.seq.course in… 

    …to davismcc-devel
    wikiselev committed Feb 5, 2018
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  4. add .Renviron to increase a max number of dlls to 250

    wikiselev committed Feb 5, 2018
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  5. Merge branch 'davismcc-devel' into devel

    wikiselev committed Feb 5, 2018
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  6. Merge branch 'devel'

    wikiselev committed Feb 5, 2018
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Commits on Feb 6, 2018

  1. update the course website

    @wikiselev
    wikiselev committed Feb 6, 2018
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Commits on Feb 7, 2018

  1. try to build an updated pdf

    wikiselev committed Feb 7, 2018
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  2. update the course website

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    wikiselev committed Feb 7, 2018
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Commits on Feb 8, 2018

  1. Add files via upload

    @tallulandrews
    tallulandrews authored Feb 8, 2018
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  2. Add files via upload

    @tallulandrews
    tallulandrews authored Feb 8, 2018
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  3. Add files via upload

    @tallulandrews
    tallulandrews authored Feb 8, 2018
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  4. add Jenkinsfile

    Vladimir Kiselev committed Feb 8, 2018
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  5. move deploy.sh to Jenkinsfile

    Vladimir Kiselev committed Feb 8, 2018
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Commits on Feb 9, 2018

  1. Add files via upload

    @tallulandrews
    tallulandrews authored Feb 9, 2018
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  2. fix latex errors

    wikiselev committed Feb 9, 2018
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  3. Merge branch 'master' of https://github.com/hemberg-lab/scRNA.seq.course

    wikiselev committed Feb 9, 2018
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  4. add triggers to the pipeline

    wikiselev committed Feb 9, 2018
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Commits on Feb 11, 2018

  1. Update 20-exprs-norm.Rmd 

    Add checking scran size factors
    @tallulandrews
    tallulandrews authored Feb 11, 2018
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Commits on Feb 12, 2018

  1. add pushing step

    wikiselev committed Feb 12, 2018
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  2. Merge branch 'master' of https://github.com/hemberg-lab/scRNA.seq.course

    wikiselev committed Feb 12, 2018
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  3. Added Jenkinsfile

    Vladimir Kiselev committed Feb 12, 2018
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Commits on Feb 13, 2018

  1. Added Jenkinsfile

    Vladimir Kiselev committed Feb 13, 2018
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  2. add base Dockerfile

    wikiselev committed Feb 13, 2018
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Commits on Feb 14, 2018

  1. delete docker-base

    wikiselev committed Feb 14, 2018
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Commits on Feb 27, 2018

  1. fix the workspace error

    wikiselev committed Feb 27, 2018
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  2. update the course website

    wikiselev committed Feb 27, 2018
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Commits on Mar 6, 2018

  1. update the course website

    wikiselev committed Mar 6, 2018
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Commits on Mar 13, 2018

  1. update the course website

    wikiselev committed Mar 13, 2018
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  2. remove pdf compilation from build

    wikiselev committed Mar 13, 2018
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  3. update the course website

    wikiselev committed Mar 13, 2018
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Commits on Mar 17, 2018

  1. try to change docker cp command

    wikiselev committed Mar 17, 2018
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  2. update the course website

    wikiselev committed Mar 17, 2018
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Commits on Mar 20, 2018

  1. update the course website

    wikiselev committed Mar 20, 2018
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  2. rm unnecessary files

    wikiselev committed Mar 20, 2018
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  3. update the course website

    wikiselev committed Mar 20, 2018
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Commits on Mar 27, 2018

  1. update the course website

    wikiselev committed Mar 27, 2018
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Commits on Apr 3, 2018

  1. update the course website

    wikiselev committed Apr 3, 2018
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Commits on Apr 10, 2018

  1. update the course website

    wikiselev committed Apr 10, 2018
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Commits on Apr 17, 2018

  1. update the course website

    wikiselev committed Apr 17, 2018
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Commits on Apr 24, 2018

  1. update the course website

    wikiselev committed Apr 24, 2018
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Commits on Apr 25, 2018

  1. add a statement about Share folder

    wikiselev committed Apr 25, 2018
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  2. update the course website

    wikiselev committed Apr 25, 2018
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Commits on Apr 26, 2018

  1. update the course website

    wikiselev committed Apr 26, 2018
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  2. add a note about Share folder

    wikiselev committed Apr 26, 2018
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  3. update the course website

    wikiselev committed Apr 26, 2018
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  4. add note

    wikiselev committed Apr 26, 2018
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  5. edit text

    wikiselev committed Apr 26, 2018
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  6. update the course website

    wikiselev committed Apr 26, 2018
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Commits on May 1, 2018

  1. update the course website

    wikiselev committed May 1, 2018
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Commits on May 8, 2018

  1. update the course website

    wikiselev committed May 8, 2018
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Commits on May 15, 2018

  1. update the course website

    wikiselev committed May 15, 2018
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Commits on May 22, 2018

  1. update the course website

    wikiselev committed May 22, 2018
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Commits on May 29, 2018

  1. update the course website

    wikiselev committed May 29, 2018
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Commits on Jun 3, 2018

  1. Proper citation for destiny

    @flying-sheep
    flying-sheep authored Jun 3, 2018
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Commits on Oct 31, 2018

  1. Turn off the progress bar for scaling procedure

    @ChuliangXiao
    ChuliangXiao authored Oct 31, 2018
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Commits on Nov 20, 2018

  1. fixed a few typos; updated code for scater plots

    @stephaniehicks
    stephaniehicks committed Nov 20, 2018
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  2. one more typo

    @stephaniehicks
    stephaniehicks committed Nov 20, 2018
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Commits on Nov 21, 2018

  1. Merge pull request #149 from flying-sheep/patch-1 

    Proper citation for destiny
    Vladimir Kiselev authored Nov 21, 2018
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  2. Merge pull request #150 from ChuliangXiao/patch-1 

    Turn off the progress bar for scaling procedure
    Vladimir Kiselev authored Nov 21, 2018
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  3. Merge pull request #152 from stephaniehicks/master 

    Fixing typos and updating code for plots in scater
    Vladimir Kiselev authored Nov 21, 2018
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