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omnideconv
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SimBu
Simulate pseudo-bulk RNAseq samples from scRNAseq expression data
http://omnideconv.org/SimBu/
GNU General Public License v3.0
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devel branch to work for GHAs
#52
federicomarini
opened
3 months ago
1
New feature: save cell-type-sepcific expression profiles
#51
FFinotello
opened
7 months ago
0
Beta Distribution to create random scenario
#50
alex-d13
opened
7 months ago
0
Merge pull request #48 from omnideconv/devel
#49
alex-d13
closed
8 months ago
0
Devel branch
#48
federicomarini
closed
8 months ago
1
Prepare for upcoming Seurat v5 release
#47
saketkc
closed
8 months ago
1
Error: BiocParallel errors 1 remote errors, element index: 1
#46
MengjurJ
opened
10 months ago
2
General questions
#45
ZheFrench
closed
10 months ago
1
Is SummarizedExperiment::assays(simulation$bulk)[["bulk_counts"]]) a raw simulated count matrix ?
#44
ZheFrench
closed
1 year ago
3
Bug in defining cell_id_col and cell_type_col in dataset_seurat function
#43
orange-whale
closed
1 year ago
1
Example/tutorial operate/access output from simulate_bulk
#42
slieped
closed
1 year ago
2
Dev
#41
alex-d13
closed
1 year ago
1
Merge recent updates to main
#40
alex-d13
closed
1 year ago
0
Mirror_db cell types are mislabeled
#39
arielah
closed
1 year ago
1
[pre-commit.ci] pre-commit autoupdate
#38
pre-commit-ci[bot]
opened
1 year ago
1
Dev
#37
alex-d13
closed
1 year ago
0
use donttest; version bump 0.99.13
#36
alex-d13
closed
1 year ago
0
0.99.12
#35
alex-d13
closed
1 year ago
0
0.99.11
#34
alex-d13
closed
1 year ago
0
versioning
#33
grst
closed
2 years ago
2
Long tests, minor edits, version bump 0.99.10
#32
alex-d13
closed
1 year ago
0
CI update
#31
grst
closed
1 year ago
7
SummarizedExperiment as input format
#30
alex-d13
opened
2 years ago
0
Creating a dataset with Seurat object asks for tpm_assay
#29
alex-d13
closed
2 years ago
0
Error while downloading datasets from Sfaira
#28
AlmogAngel
opened
2 years ago
7
Simbu website
#27
grst
closed
2 years ago
1
Update check-standard.yaml
#26
alex-d13
closed
2 years ago
0
Manuscript Figure 4
#25
alex-d13
closed
2 years ago
6
Manuscript Figure 3
#24
alex-d13
closed
2 years ago
13
Manuscript Figure 2
#23
alex-d13
closed
2 years ago
10
Manuscript Figure1
#22
alex-d13
closed
2 years ago
7
Adding a TODO md file to track the potential issues - before submission to Bioconductor.
#21
federicomarini
closed
2 years ago
3
Manuscript figures
#20
alex-d13
closed
2 years ago
21
mRNA bias in SimBu
#19
FFinotello
closed
2 years ago
5
Dev
#18
alex-d13
closed
2 years ago
0
Sfaira changes
#17
alex-d13
closed
2 years ago
0
Publication
#16
mlist
closed
2 years ago
1
Package improvements
#15
alex-d13
closed
2 years ago
9
only use high confidence cells
#14
grst
closed
2 years ago
4
Get "spike-in" estimate from 10x protocol
#13
grst
closed
2 years ago
0
transfer website to gh-pages branch of this repo
#12
grst
closed
2 years ago
0
Count diagnostics
#11
alex-d13
closed
2 years ago
10
Simulation results
#10
alex-d13
closed
2 years ago
54
Vignette
#9
FFinotello
closed
2 years ago
6
package installation and documenation
#8
grst
closed
2 years ago
4
more simulation scenarios
#7
grst
closed
2 years ago
0
K-mer signatures
#6
FFinotello
closed
2 years ago
2
Simulation Implementation
#5
alex-d13
closed
2 years ago
23
Simulation inputs and options
#4
FFinotello
closed
2 years ago
2
Sanity check: mRNA contents
#3
grst
closed
2 years ago
19
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