Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

2020update #169

Open
wants to merge 962 commits into
base: master
Choose a base branch
from
Open
Changes from 1 commit
Commits
Show all changes
962 commits
Select commit Hold shift + click to select a range
a58c5a1
try rstudio folder
wikiselev Oct 26, 2017
0b43c0b
update docker and its information
wikiselev Oct 26, 2017
cef9d2e
fix sildist bug in SC3
wikiselev Oct 27, 2017
1a6a92e
fix cluster installation
wikiselev Oct 27, 2017
ea063bb
add projection; fix M3Drop bug
wikiselev Oct 27, 2017
a2f178a
update index; switch off half of the chapters
wikiselev Oct 27, 2017
5066b38
move snn-cliq and MAGIC to utils
wikiselev Oct 27, 2017
5a14f2d
fix last chapters
wikiselev Oct 27, 2017
e8d404c
activate first chapters
wikiselev Oct 27, 2017
57a1e85
update README
wikiselev Oct 27, 2017
8b1ecd4
fix imputation, update chapter numbers
wikiselev Oct 27, 2017
b56a1c5
add scfind
wikiselev Oct 27, 2017
7865364
update the course website
wikiselev Oct 27, 2017
13323af
update the course website
wikiselev Oct 27, 2017
757b0d5
polishing up to chapter 11 inclusive
wikiselev Oct 27, 2017
9b52c89
Update 21-imputation.Rmd
Oct 27, 2017
541994d
Merge branch 'master' of https://github.com/hemberg-lab/scRNA.seq.course
wikiselev Oct 27, 2017
7d6d6c6
Merge pull request #128 from hemberg-lab/mhemberg-patch-1
Oct 27, 2017
acc010a
Merge branch 'master' of https://github.com/hemberg-lab/scRNA.seq.course
wikiselev Oct 27, 2017
6d8065c
update imputation
wikiselev Oct 27, 2017
c002009
update imputation
wikiselev Oct 27, 2017
b87c443
update seurat
wikiselev Oct 27, 2017
eecc91e
add limma
wikiselev Oct 28, 2017
8e591e7
fix chapter 8
wikiselev Oct 28, 2017
d4bba17
update the course website
wikiselev Oct 28, 2017
9131dec
update the course website
wikiselev Oct 28, 2017
e15cd89
update expression chapter; some minor updates
wikiselev Oct 28, 2017
5762bc4
Merge branch 'master' of https://github.com/hemberg-lab/scRNA.seq.course
wikiselev Oct 28, 2017
70e1608
add ARI; minor updates
wikiselev Oct 28, 2017
3a6fcdc
update the course website
wikiselev Oct 29, 2017
02b60a8
activate pdf building again
wikiselev Oct 29, 2017
d77e503
Merge branch 'master' of https://github.com/hemberg-lab/scRNA.seq.course
wikiselev Oct 29, 2017
94e13e8
update the course website
wikiselev Oct 29, 2017
a957fca
update the course website
wikiselev Oct 29, 2017
307b19f
update bib file with betterbib tool
wikiselev Oct 29, 2017
dbdb2de
Merge branch 'master' of https://github.com/hemberg-lab/scRNA.seq.course
wikiselev Oct 29, 2017
64794b8
update the course website
wikiselev Oct 29, 2017
02b882b
Update 27-ideal-scrnaseq-pipeline.Rmd
tallulandrews Oct 30, 2017
6bb64c5
Merge branch 'tallulandrews-patch-1'
wikiselev Oct 30, 2017
15ea384
minor text updates
wikiselev Oct 30, 2017
2d2fab1
Fixed typos
Oct 30, 2017
b97c8f5
Merge branch 'master' of https://github.com/hemberg-lab/scRNA.seq.course
wikiselev Oct 30, 2017
eea0ad5
Fixed typos
Oct 30, 2017
f95ba27
Fixed text
Oct 30, 2017
d080cfc
Fixed typos
Oct 30, 2017
a52f967
Minor fixes
Oct 30, 2017
b280ebd
Fixed typo
Oct 30, 2017
f3c215f
Minor changes
Oct 30, 2017
ea0682b
Merge branch 'master' into mhemberg-patch-1
wikiselev Oct 30, 2017
8163e55
Merge branch 'mhemberg-patch-1'
wikiselev Oct 30, 2017
505d97c
Merge branch 'master' into mhemberg-patch-2
wikiselev Oct 30, 2017
8db61c2
Merge branch 'mhemberg-patch-2'
wikiselev Oct 30, 2017
58f48b7
Merge branch 'master' into mhemberg-patch-3
wikiselev Oct 30, 2017
17f7b22
Merge branch 'mhemberg-patch-3'
wikiselev Oct 30, 2017
23eddcc
Merge branch 'master' into mhemberg-patch-4
wikiselev Oct 30, 2017
e9498ae
Merge branch 'mhemberg-patch-4'
wikiselev Oct 30, 2017
8695f55
Merge branch 'master' into mhemberg-patch-5
wikiselev Oct 30, 2017
dc64dd0
Merge branch 'mhemberg-patch-5'
wikiselev Oct 30, 2017
56b54b4
final updates
wikiselev Oct 30, 2017
9f48740
Merge branch 'mhemberg-patch-6'
wikiselev Oct 30, 2017
f77d10e
update the course website
wikiselev Oct 30, 2017
32830fa
switch off pdf building
wikiselev Oct 30, 2017
4850f26
update the course website
wikiselev Oct 31, 2017
5b75630
update the course website
wikiselev Nov 1, 2017
43ebe8c
Add exercise solutions
tallulandrews Nov 1, 2017
2171955
update index page
wikiselev Nov 2, 2017
25fc479
move to Bioconductor release branch
wikiselev Nov 2, 2017
b61ff94
Merge branch 'master' of github.com:hemberg-lab/scRNA.seq.course
wikiselev Nov 2, 2017
cd6891e
add RUVSeq dependency
wikiselev Nov 6, 2017
27ff0af
trying to fix RMySQL
wikiselev Nov 6, 2017
6f4278c
Fix dropout chapter
wikiselev Nov 7, 2017
e9c4f6f
update the course website
wikiselev Nov 7, 2017
6e71f2b
update the course website
wikiselev Nov 7, 2017
adb168e
update the course website
wikiselev Nov 8, 2017
0139493
update the course website
wikiselev Nov 9, 2017
224e41e
update the course website
wikiselev Nov 10, 2017
51bd31b
update the course website
wikiselev Nov 11, 2017
8aa5667
update the course website
wikiselev Nov 12, 2017
0971962
update the course website
wikiselev Nov 13, 2017
386ce57
update the course website
wikiselev Nov 14, 2017
c571626
update the course website
wikiselev Nov 15, 2017
3f4864c
update the course website
wikiselev Nov 16, 2017
bc8c8ed
update the course website
wikiselev Nov 18, 2017
83ef4b0
update the course website
wikiselev Nov 19, 2017
7df2e57
update the course website
wikiselev Nov 20, 2017
60e629a
update the course website
wikiselev Nov 22, 2017
57ec956
update the course website
wikiselev Nov 23, 2017
b66117e
fix pseudotime chapter
wikiselev Nov 24, 2017
dbb71a7
Fix mnn_correct issues; update Youtube link on the main page
wikiselev Dec 11, 2017
e75c4f6
fix mnnCorrect problem for reads
wikiselev Dec 13, 2017
fc79472
switch off normalisatio by gene length (it's wrong and biomaRt call f…
wikiselev Dec 18, 2017
d192598
forgot to add eval=FALSE
Dec 19, 2017
7b2e01c
Add Lab5 - download Tabula Muris
tallulandrews Jan 11, 2018
6f2862d
First half of introduction to R lab
tallulandrews Jan 12, 2018
a69e8e4
First half of introduction to R lab
tallulandrews Jan 12, 2018
a2cf8de
Delete L3-intro-to-R.Rmd
tallulandrews Jan 12, 2018
869f64b
Add colour explanation
tallulandrews Jan 12, 2018
6818d6d
Update L3-intro-to-R.Rmd
tallulandrews Jan 12, 2018
50573fc
feature_symbol is requried in the newest version of SC3
Jan 14, 2018
189a256
Merge branch 'master' of github.com:hemberg-lab/scRNA.seq.course
Jan 14, 2018
559f661
First half of processing raw data lab
tallulandrews Jan 15, 2018
6125940
add mnnCorrect diagram
tallulandrews Jan 16, 2018
c21b2ca
fix imputation and scmap
Jan 16, 2018
6efd273
Update 24-projection.Rmd
tallulandrews Jan 16, 2018
fe8289a
CCA (Seurat) plots
tallulandrews Jan 16, 2018
433a5ee
New Cross-dataset diagrams
tallulandrews Jan 16, 2018
dfb9985
Update 24-projection.Rmd
tallulandrews Jan 16, 2018
b9c181b
update the course website
wikiselev Jan 17, 2018
8eb19ee
update the course website
wikiselev Jan 17, 2018
eb652eb
JW first draft of reads QC lab 1
Jan 18, 2018
354d9e6
update the course website
wikiselev Jan 18, 2018
2ef8920
JW added wget commands to download Kolod et al. data
Jan 18, 2018
40fdb8b
JW first draft of alignment lab including images used in Rmd
Jan 18, 2018
a2290b7
update the course website
wikiselev Jan 19, 2018
5ae1aff
update the course website
wikiselev Jan 20, 2018
dd905af
update the course website
wikiselev Jan 21, 2018
05de376
update Dockerfile, add processing software
Jan 21, 2018
3ee0e25
Merge branch 'master' of github.com:hemberg-lab/scRNA.seq.course
Jan 21, 2018
6f1eab3
add curl
Jan 21, 2018
cedc4e0
fix R packages installation
Jan 21, 2018
2e277d2
add fastqc, kallisto, bedtools2 and cutadapt
Jan 22, 2018
f5c7db8
update the course website
wikiselev Jan 22, 2018
8948940
fix bedtools; remove unnessesary software
Jan 23, 2018
98607d6
Merge branch 'master' of github.com:hemberg-lab/scRNA.seq.course
Jan 23, 2018
bd6f9ba
fix bedtools again
Jan 23, 2018
3937a34
update the course website
wikiselev Jan 23, 2018
ed8e28d
fix kallisto; update README
Jan 24, 2018
7ed3d37
Merge branch 'master' of github.com:hemberg-lab/scRNA.seq.course
Jan 24, 2018
5c58349
update the course website
wikiselev Jan 24, 2018
9c06e14
add tidyverse and ggfortify
Jan 25, 2018
1fa4199
Merge branch 'master' of github.com:hemberg-lab/scRNA.seq.course
Jan 25, 2018
2a6f1c4
Upload 2000 transcript transcriptome -JW
Jan 25, 2018
be9d67a
update the course website
wikiselev Jan 25, 2018
aca6dc0
All files checked against docker image except L4 - JW
Jan 26, 2018
cc74252
update the course website
wikiselev Jan 26, 2018
cc4ffb7
update the course website
wikiselev Jan 27, 2018
ef214e0
Add demultiplexing lab
tallulandrews Jan 28, 2018
6655525
Update L3-intro-to-R.Rmd
tallulandrews Jan 28, 2018
2fa7a9c
demultiplexing example data
tallulandrews Jan 29, 2018
0f7ecfa
ID true cell barcodes example data
tallulandrews Jan 29, 2018
1c51597
merge new chapters from devel branch
Jan 30, 2018
e7eae87
update the course website
wikiselev Jan 30, 2018
ba952f7
remove empty continuation lines
Jan 31, 2018
fd999b2
Merge branch 'master' of github.com:hemberg-lab/scRNA.seq.course
Jan 31, 2018
0980850
update the course website
wikiselev Jan 31, 2018
600db99
order chapters
Jan 31, 2018
2231be2
Merge branch 'master' of github.com:hemberg-lab/scRNA.seq.course
Jan 31, 2018
094f940
Update 05-L1-process-raw.Rmd
tallulandrews Feb 1, 2018
a73df46
Update 30-de-real.Rmd
tallulandrews Feb 1, 2018
86d1c11
install trim_galore; minor edits
Feb 1, 2018
4d37ad2
Update 05-L1-process-raw.Rmd
tallulandrews Feb 1, 2018
b591c37
update trim_galore link
Feb 1, 2018
a9cbb63
Add demultiplexing perl scripts
tallulandrews Feb 1, 2018
28f04d6
Merge branch 'devel' of github.com:hemberg-lab/scRNA.seq.course into …
Feb 1, 2018
d157852
Merge branch 'devel' of github.com:hemberg-lab/scRNA.seq.course into …
Feb 1, 2018
97aa461
Update 05-L1-process-raw.Rmd
tallulandrews Feb 1, 2018
f78ca04
Update 06-L1-process-raw-align.Rmd
tallulandrews Feb 1, 2018
c339052
Update 09-L3-intro-to-R.Rmd
tallulandrews Feb 1, 2018
d76f481
Update 13-L5-Intro-TabulaMuris.Rmd
tallulandrews Feb 1, 2018
b69800c
split dockerfile in two
Feb 1, 2018
3c7c977
Merge branch 'devel' of github.com:hemberg-lab/scRNA.seq.course into …
Feb 1, 2018
bb10cea
Merge branch 'master' of github.com:hemberg-lab/scRNA.seq.course
Feb 1, 2018
b2ed408
update Dockerfile
Feb 1, 2018
d4ceec9
remove less
Feb 2, 2018
1b092a4
Add metaneighbour
tallulandrews Feb 2, 2018
69fffd1
Update 31-projection.Rmd
tallulandrews Feb 2, 2018
c3a6330
update the course website
wikiselev Feb 2, 2018
8d0bd5b
Update 05-L1-process-raw.Rmd
tallulandrews Feb 2, 2018
9df0c1e
Update 13-L5-Intro-TabulaMuris.Rmd
tallulandrews Feb 2, 2018
8fd3d68
Update 14-exprs-qc.Rmd
tallulandrews Feb 2, 2018
256d329
JW fixed references and tested code on AWS
Feb 2, 2018
e0f8c88
JW fixed references and tested code on AWS
Feb 2, 2018
cc722fa
Merge branch 'devel' of https://github.com/hemberg-lab/scRNA.seq.course
Feb 2, 2018
857be2d
Merge branch 'devel'
Feb 2, 2018
44c070d
Merge branch 'devel'
Feb 2, 2018
55dd29f
update the course website
wikiselev Feb 2, 2018
8a5482d
update the headers
Feb 2, 2018
28e9d3b
update main page, clean the docs folder
Feb 2, 2018
23f334e
update README; add empty-file to docs
Feb 2, 2018
fec0b01
remove year
Feb 2, 2018
ba5af60
update the course website
wikiselev Feb 2, 2018
6cedbcc
fix some outputs
Feb 2, 2018
176da10
Merge branch 'master' of github.com:hemberg-lab/scRNA.seq.course
Feb 2, 2018
2092837
update the course website
wikiselev Feb 2, 2018
ccee30f
update the course website
wikiselev Feb 3, 2018
dbb2b2f
hide projection chapter
Feb 3, 2018
96cfae2
Merge branch 'master' of github.com:hemberg-lab/scRNA.seq.course
Feb 3, 2018
9d04274
update the course website
wikiselev Feb 3, 2018
90ca80c
update the course website
wikiselev Feb 4, 2018
bb0405c
Updating pseudotime chapter.
davismcc Feb 5, 2018
b6f231f
update the course website
wikiselev Feb 5, 2018
6a33c86
Merge branch 'devel' of git://github.com/davismcc/scRNA.seq.course in…
Feb 5, 2018
ecdd535
add .Renviron to increase a max number of dlls to 250
Feb 5, 2018
67700bf
Merge branch 'davismcc-devel' into devel
Feb 5, 2018
dff9b75
Merge branch 'devel'
Feb 5, 2018
bb223e3
update the course website
wikiselev Feb 6, 2018
fc297bb
try to build an updated pdf
Feb 7, 2018
0732b2a
update the course website
wikiselev Feb 7, 2018
1686056
Add files via upload
tallulandrews Feb 8, 2018
43a2249
Add files via upload
tallulandrews Feb 8, 2018
e455cc2
Add files via upload
tallulandrews Feb 8, 2018
83c41a8
add Jenkinsfile
Feb 8, 2018
4f0f036
move deploy.sh to Jenkinsfile
Feb 8, 2018
e502bea
Add files via upload
tallulandrews Feb 9, 2018
f943448
fix latex errors
Feb 9, 2018
5a43a18
Merge branch 'master' of https://github.com/hemberg-lab/scRNA.seq.course
Feb 9, 2018
0a54c68
add triggers to the pipeline
Feb 9, 2018
862631d
Update 20-exprs-norm.Rmd
tallulandrews Feb 11, 2018
b090c24
add pushing step
Feb 12, 2018
ee85712
Merge branch 'master' of https://github.com/hemberg-lab/scRNA.seq.course
Feb 12, 2018
278a19a
Added Jenkinsfile
Feb 12, 2018
ab6e57b
Added Jenkinsfile
Feb 13, 2018
0333756
add base Dockerfile
Feb 13, 2018
2b3e2d0
delete docker-base
Feb 14, 2018
77319b7
fix the workspace error
Feb 27, 2018
a3500fe
update the course website
Feb 27, 2018
20d791c
update the course website
Mar 6, 2018
e400eab
update the course website
Mar 13, 2018
030a0df
remove pdf compilation from build
Mar 13, 2018
0ad0cdf
update the course website
Mar 13, 2018
b06062b
try to change docker cp command
Mar 17, 2018
d42f56b
update the course website
Mar 17, 2018
b2a1998
update the course website
Mar 20, 2018
8a3b775
rm unnecessary files
Mar 20, 2018
1ee9ac6
update the course website
Mar 20, 2018
854cce1
update the course website
Mar 27, 2018
934127b
update the course website
Apr 3, 2018
4537e9c
update the course website
Apr 10, 2018
4b4bc1c
update the course website
Apr 17, 2018
1b67fa6
update the course website
Apr 24, 2018
5922b46
add a statement about Share folder
Apr 25, 2018
198081c
update the course website
Apr 25, 2018
a6eb8a6
update the course website
Apr 26, 2018
6b9a453
add a note about Share folder
Apr 26, 2018
b3862fb
update the course website
Apr 26, 2018
570c954
add note
Apr 26, 2018
ddc9968
edit text
Apr 26, 2018
4cd1013
update the course website
Apr 26, 2018
93a2c30
update the course website
May 1, 2018
1260438
update the course website
May 8, 2018
d81fa44
update the course website
May 15, 2018
fcd70c8
update the course website
May 22, 2018
7a36651
update the course website
May 29, 2018
b64c48e
Proper citation for destiny
flying-sheep Jun 3, 2018
7e82e5d
Turn off the progress bar for scaling procedure
ChuliangXiao Oct 31, 2018
d33bd9d
fixed a few typos; updated code for scater plots
stephaniehicks Nov 20, 2018
fd17135
one more typo
stephaniehicks Nov 20, 2018
52a2359
Merge pull request #149 from flying-sheep/patch-1
Nov 21, 2018
ccadb22
Merge pull request #150 from ChuliangXiao/patch-1
Nov 21, 2018
aa3222f
Merge pull request #152 from stephaniehicks/master
Nov 21, 2018
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
Prev Previous commit
Next Next commit
Add files via upload
tallulandrews authored Feb 9, 2018
commit e502bea7e16e96ca406fdad7d19c671a15768be0
Binary file added Lecture_ExperimentalDesign.pdf
Binary file not shown.