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Cibersort check 0 counts #218

Merged
merged 59 commits into from
Nov 8, 2021
Merged

Cibersort check 0 counts #218

merged 59 commits into from
Nov 8, 2021

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stemangiola
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stemangiola and others added 30 commits July 13, 2021 16:25
@stemangiola
Merge pull request #196 from stemangiola/dev
bb526a3 
Dev
@stemangiola
version UP
aaf69e2
@stemangiola
Merge pull request #199 from stemangiola/dev
e442d4a 
Dev
@stemangiola
Merge pull request #202 from stemangiola/scale-with-house-keeping
b646de1 
Scale with house keeping
@stemangiola
Merge pull request #203 from stemangiola/dev
a1c2ccb 
Dev
@stemangiola
Update DESCRIPTION
8dcb0aa
@stemangiola
Merge pull request #206 from stemangiola/dev
b3e55ba 
Dev
@stemangiola
Version UP + NEWS
820b0b8
@stemangiola
Merge pull request #216 from stemangiola/dev
065646e 
Dev
@stemangiola
drop Impute missing test
c2c55b0
@stemangiola
add intercept argument for llsr in case the X matrix is colinear
af9afea
@stemangiola
update cibersort with filtering
78858b5
@stemangiola
avoid exp transformation for single-cell
77e4f51
@stemangiola
make exp transformation false by default
dc38782
@stemangiola
fix tests
1bdbeff
@stemangiola
fix docs
cbbdd6d
@stemangiola
avoid example as failing on windows Bioconductor CHECK
e30b102
@stemangiola
try to solve bioc check https://master.bioconductor.org/checkResults/…
a4872cd 
…3.14/bioc-LATEST/tidybulk/nebbiolo2-buildsrc.html
@stemangiola
avoid error for Bioc CHECK
8561118
@stemangiola
try to fix Bioconductor CHECK
b32e3ff
@mblue9
Update NEWS.rd
1f9a5d7
@stemangiola
try to fix error Bioc
1c12b68
@stemangiola
version UP
7110cae
@nturaga
bump x.y.z version to even y prior to creation of RELEASE_3_14 branch
ef70153
@stemangiola
Update issue templates
937fa06
@stemangiola
update README
efda705
@stemangiola
Merge branch 'master' of github.com:stemangiola/tidybulk
087618f
@stemangiola
update README and bug report
64bc7f2 
Merge branch 'master' into RELEASE_3_14

# Please enter a commit message to explain why this merge is necessary,
# especially if it merges an updated upstream into a topic branch.
#
# Lines starting with '#' will be ignored, and an empty message aborts
# the commit.
@stemangiola
pull from RELEASE_3_14
f1aa54a 
Merge branch 'RELEASE_3_14' of git.bioconductor.org:packages/tidybulk into RELEASE_3_14

# Please enter a commit message to explain why this merge is necessary,
# especially if it merges an updated upstream into a topic branch.
#
# Lines starting with '#' will be ignored, and an empty message aborts
# the commit.
@stemangiola
version UP
13706d8
antass and others added 29 commits November 1, 2021 12:22
@antass
Fix typo in DESeq raw result return
220c90c
@stemangiola
Merge pull request #220 from stemangiola/mblue9-patch-3
115e368 
Update NEWS.rd
@stemangiola
Merge pull request #223 from antass/patch-1
46d4856 
Fix typo in DESeq raw result variable return
@stemangiola
print message if reference is not defined by the user
bc33d90
@stemangiola
make some other messages only once
c923ff1
@stemangiola
Merge pull request #226 from stemangiola/message-for-scaling-reference
992a512 
print message if reference is not defined by the user
@stemangiola
try to fix CHECKs
3068312
@stemangiola
fix tests, llsr deconvolution has a different outcome because now it …
a01ed52 
…has intercept = TRUE, for avoiding singular matrices. This means that is modelling a background cell population.
@stemangiola
print message if reference is not defined by the user
7d3c418
@stemangiola
make some other messages only once
edc1882
@stemangiola
Merge branch 'dev' of github.com:stemangiola/tidybulk into dev
41ba606
@stemangiola
try to fix tests
c557c92
@stemangiola
fix Y filtering cibersort
e2b3273
@stemangiola
strange different OS have such different results
d4ad78b
@stemangiola
add intercept argument for llsr in case the X matrix is colinear
618a8a9
@stemangiola
update cibersort with filtering
519dbd0
@stemangiola
avoid exp transformation for single-cell
ef1293c
@stemangiola
make exp transformation false by default
36688c7
@stemangiola
fix tests
c01010f
@stemangiola
fix docs
2dfc4a5
@stemangiola
try to fix CHECKs
8049fea
@stemangiola
fix tests, llsr deconvolution has a different outcome because now it …
d9d9e86 
…has intercept = TRUE, for avoiding singular matrices. This means that is modelling a background cell population.
@stemangiola
try to fix tests
4e10c89
@stemangiola
fix Y filtering cibersort
70a9c0b
@stemangiola
strange different OS have such different results
2baf6da
@stemangiola
pull
036087f 
Merge branch 'cibersort-check-0-counts' of github.com:stemangiola/tidybulk into cibersort-check-0-counts

Conflicts:
	DESCRIPTION
@stemangiola
fix test for deconvolution
cc10355
@stemangiola
fix dependency
0f145e8
@stemangiola
add igraph dependency
fd0d66c
@stemangiola stemangiola merged commit ade7eef into dev Nov 8, 2021
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4 participants
@stemangiola @mblue9 @nturaga @antass