GitHub / omnideconv/SimBu issues and pull requests

#53 - samples vs simulations

Issue - State: closed - Opened by mea2712 about 1 year ago - 2 comments
Labels: question

#52 - devel branch to work for GHAs

Pull Request - State: open - Opened by federicomarini over 1 year ago - 1 comment

#51 - New feature: save cell-type-sepcific expression profiles

Issue - State: open - Opened by FFinotello over 1 year ago - 1 comment
Labels: enhancement

#50 - Beta Distribution to create random scenario

Issue - State: open - Opened by alex-d13 over 1 year ago
Labels: enhancement

#49 - Merge pull request #48 from omnideconv/devel

Pull Request - State: closed - Opened by alex-d13 over 1 year ago

#48 - Devel branch

Pull Request - State: closed - Opened by federicomarini almost 2 years ago - 1 comment

#47 - Prepare for upcoming Seurat v5 release

Issue - State: closed - Opened by saketkc almost 2 years ago - 1 comment

#46 - Error: BiocParallel errors 1 remote errors, element index: 1

Issue - State: open - Opened by MengjurJ almost 2 years ago - 2 comments

#45 - General questions

Issue - State: closed - Opened by ZheFrench over 2 years ago - 1 comment

#44 - Is SummarizedExperiment::assays(simulation$bulk)[["bulk_counts"]]) a raw simulated count matrix ?

Issue - State: closed - Opened by ZheFrench over 2 years ago - 3 comments
Labels: question

#43 - Bug in defining cell_id_col and cell_type_col in dataset_seurat function

Issue - State: closed - Opened by orange-whale over 2 years ago - 1 comment

#42 - Example/tutorial operate/access output from simulate_bulk

Issue - State: closed - Opened by slieped over 2 years ago - 2 comments

#41 - Dev

Pull Request - State: closed - Opened by alex-d13 almost 3 years ago - 1 comment

#40 - Merge recent updates to main

Pull Request - State: closed - Opened by alex-d13 almost 3 years ago

#39 - Mirror_db cell types are mislabeled

Issue - State: closed - Opened by arielah almost 3 years ago - 1 comment
Labels: bug

#38 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: open - Opened by pre-commit-ci[bot] almost 3 years ago - 1 comment

#37 - Dev

Pull Request - State: closed - Opened by alex-d13 about 3 years ago

#36 - use donttest; version bump 0.99.13

Pull Request - State: closed - Opened by alex-d13 about 3 years ago

#35 - 0.99.12

Pull Request - State: closed - Opened by alex-d13 about 3 years ago

#34 - 0.99.11

Pull Request - State: closed - Opened by alex-d13 about 3 years ago

#33 - versioning

Issue - State: closed - Opened by grst about 3 years ago - 2 comments

#32 - Long tests, minor edits, version bump 0.99.10

Pull Request - State: closed - Opened by alex-d13 about 3 years ago

#31 - CI update

Pull Request - State: closed - Opened by grst about 3 years ago - 7 comments

#30 - SummarizedExperiment as input format

Issue - State: open - Opened by alex-d13 about 3 years ago
Labels: enhancement

#29 - Creating a dataset with Seurat object asks for tpm_assay

Issue - State: closed - Opened by alex-d13 about 3 years ago
Labels: bug

#28 - Error while downloading datasets from Sfaira

Issue - State: open - Opened by AlmogAngel about 3 years ago - 7 comments
Labels: bug

#27 - Simbu website

Issue - State: closed - Opened by grst about 3 years ago - 1 comment

#26 - Update check-standard.yaml

Pull Request - State: closed - Opened by alex-d13 over 3 years ago

#25 - Manuscript Figure 4

Issue - State: closed - Opened by alex-d13 over 3 years ago - 6 comments

#24 - Manuscript Figure 3

Issue - State: closed - Opened by alex-d13 over 3 years ago - 13 comments

#23 - Manuscript Figure 2

Issue - State: closed - Opened by alex-d13 over 3 years ago - 10 comments

#22 - Manuscript Figure1

Issue - State: closed - Opened by alex-d13 over 3 years ago - 7 comments

#21 - Adding a TODO md file to track the potential issues - before submission to Bioconductor.

Pull Request - State: closed - Opened by federicomarini over 3 years ago - 3 comments

#20 - Manuscript figures

Issue - State: closed - Opened by alex-d13 over 3 years ago - 21 comments

#19 - mRNA bias in SimBu

Issue - State: closed - Opened by FFinotello over 3 years ago - 5 comments

#18 - Dev

Pull Request - State: closed - Opened by alex-d13 over 3 years ago

#17 - Sfaira changes

Pull Request - State: closed - Opened by alex-d13 over 3 years ago

#16 - Publication

Issue - State: closed - Opened by mlist over 3 years ago - 1 comment

#15 - Package improvements

Issue - State: closed - Opened by alex-d13 over 3 years ago - 9 comments

#14 - only use high confidence cells

Issue - State: closed - Opened by grst over 3 years ago - 4 comments

#13 - Get "spike-in" estimate from 10x protocol

Issue - State: closed - Opened by grst over 3 years ago

#12 - transfer website to gh-pages branch of this repo

Issue - State: closed - Opened by grst over 3 years ago

#11 - Count diagnostics

Issue - State: closed - Opened by alex-d13 over 3 years ago - 10 comments

#10 - Simulation results

Issue - State: closed - Opened by alex-d13 over 3 years ago - 54 comments

#9 - Vignette

Issue - State: closed - Opened by FFinotello almost 4 years ago - 6 comments

#8 - package installation and documenation

Issue - State: closed - Opened by grst almost 4 years ago - 4 comments

#7 - more simulation scenarios

Issue - State: closed - Opened by grst almost 4 years ago

#6 - K-mer signatures

Issue - State: closed - Opened by FFinotello almost 4 years ago - 2 comments

#5 - Simulation Implementation

Issue - State: closed - Opened by alex-d13 almost 4 years ago - 23 comments

#4 - Simulation inputs and options

Issue - State: closed - Opened by FFinotello about 4 years ago - 2 comments

#3 - Sanity check: mRNA contents

Issue - State: closed - Opened by grst about 4 years ago - 19 comments

#2 - Simulation Strategy

Issue - State: closed - Opened by alex-d13 about 4 years ago - 52 comments

#1 - Datasets

Issue - State: closed - Opened by alex-d13 about 4 years ago - 3 comments