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combiz
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scFlow
Single-cell/nuclei RNA-seq analysis tools in R for a complete workflow.
https://combiz.github.io/scFlow/
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[Feature]
#206
nasjr08
closed
2 weeks ago
0
[bug] Error while running perform_de() function
#205
vd4mmind
opened
7 months ago
0
[bug] Error with UMAP plot generation
#204
vd4mmind
opened
7 months ago
1
[bug] Issue with report generation from vignette
#203
vd4mmind
closed
7 months ago
1
Update README.md
#202
nfancy
opened
7 months ago
0
Dev
#201
combiz
closed
7 months ago
0
Updated DoubletFinder function
#200
nfancy
closed
7 months ago
0
DoubletFinder function names have changed [bug]
#199
CharlotteAnne
closed
7 months ago
2
Dev
#198
combiz
closed
8 months ago
0
Dev nf
#197
nfancy
closed
1 year ago
0
[bug]
#196
ipiras
closed
1 year ago
0
matrix files gets changed during 'Reading feature-barcode matrix'
#195
athulmenon
opened
1 year ago
1
Add scripts
#194
pinin4fjords
opened
1 year ago
0
[bug] cell type proportions approach doesn't correct for multiple testing
#193
Al-Murphy
opened
1 year ago
1
Error in file(con, "r") : cannot open the connection
#192
umranyaman
opened
1 year ago
3
EWCE
#191
umranyaman
closed
1 year ago
2
[bug] Error in download
#190
OscarW99
opened
2 years ago
0
[bug] Update EWCE for 4.2
#189
combiz
opened
2 years ago
0
feat: add option to test higher pc_mito tail
#188
RHReynolds
opened
2 years ago
0
[Feature] Permit users to decide which tails to test for mitochondrial content outlier detection
#187
RHReynolds
opened
2 years ago
0
Dockerfile fails to build due to code/documentation mismatches in R CMD check
#186
RHReynolds
closed
2 years ago
7
[Feature] Incorporate LIANA for cross-talk analysis
#185
combiz
opened
3 years ago
0
Update issue templates
#184
combiz
closed
3 years ago
0
Update issue templates
#183
combiz
closed
3 years ago
0
Dev
#182
combiz
closed
3 years ago
0
Include point size and alpha global variables for plotting
#181
combiz
closed
3 years ago
1
Auto install bioc dependencies with github install
#180
Al-Murphy
closed
3 years ago
2
Add GHA badge
#179
Al-Murphy
closed
3 years ago
0
PR Updates
#178
Al-Murphy
closed
3 years ago
0
Dev am
#177
Al-Murphy
closed
3 years ago
0
read_metadata errors with "adding class "factor" to invalid object"
#175
combiz
closed
3 years ago
0
improved liger & IPA codes
#174
nfancy
closed
3 years ago
0
Dirichlet report needs a summary figure
#173
NathanSkene
closed
3 years ago
1
Docker build file must be on github + setup so that it rebuilds on Dockerhub every time there are changes on github
#172
NathanSkene
closed
3 years ago
1
Add the old manual to the current vignette to explain how to use the scFlow R package functions
#171
NathanSkene
closed
3 years ago
0
Resolve issue that means differential expressions steps of the NextFlow pipeline don't get run
#170
NathanSkene
closed
3 years ago
0
Get 6.0.2 onto dockerhub
#169
NathanSkene
closed
3 years ago
0
Fails on EWCE mapping cell-typing while running on mouse datasets
#168
NathanSkene
closed
3 years ago
0
No mitochondrial genes detected when running on mouse datasets
#167
NathanSkene
closed
3 years ago
0
Nurun's zip file with everything needed to test the pipeline should be available through figshare such that it is compatible with the NF-core tutorial dataset standards
#166
NathanSkene
closed
3 years ago
0
Add gene_biotype filtering
#165
combiz
closed
3 years ago
0
Add option to keep specific gene_biotype
#164
combiz
closed
3 years ago
0
Add option to use HPF instead of PCA throughout
#163
NathanSkene
closed
3 years ago
0
Test whether automated cell-typing works for iPSC cultured neurons. Ernest Arenas is interested in whether we can do this. Could be a good figure for the paper.
#162
NathanSkene
closed
3 years ago
0
Enable the pipeline to save data in format suitable for upload to the Broad's Single Cell Portal / CellXGene
#161
NathanSkene
closed
4 years ago
1
Resolve issue that lead to Lynn's run crashing due to graphviz
#160
NathanSkene
closed
3 years ago
1
Miniconda should already be set up within the docker image so that it doesn't ask for it to be installed when library(scFlow) is run within the image
#159
NathanSkene
closed
4 years ago
1
In the cell type report, list the top EWCE probabilities for each cell type. So that you can see if a cluster has highP for oligos and neurons.
#158
NathanSkene
closed
3 years ago
1
Add adaptive upper threshold for pc_mito cut-off
#157
nfancy
closed
3 years ago
0
updated integrate annotation and report
#156
MahdiMoradiMarjaneh
opened
4 years ago
0
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