Issues
- 0
- 0
[bug] Error while running perform_de() function
#205 opened by vd4mmind - 1
[bug] Error with UMAP plot generation
#204 opened by vd4mmind - 1
[bug] Issue with report generation from vignette
#203 opened by vd4mmind - 2
DoubletFinder function names have changed [bug]
#199 opened by CharlotteAnne - 1
- 0
- 1
- 3
- 2
EWCE
#191 opened by umranyaman - 0
[bug] Error in download
#190 opened by OscarW99 - 0
[bug] Update EWCE for 4.2
#189 opened by combiz - 0
[Feature] Permit users to decide which tails to test for mitochondrial content outlier detection
#187 opened by RHReynolds - 7
Dockerfile fails to build due to code/documentation mismatches in R CMD check
#186 opened by RHReynolds - 0
[Feature] Incorporate LIANA for cross-talk analysis
#185 opened by combiz - 0
Resolve issue that means differential expressions steps of the NextFlow pipeline don't get run
#170 opened by NathanSkene - 0
Add the old manual to the current vignette to explain how to use the scFlow R package functions
#171 opened by NathanSkene - 1
Dirichlet report needs a summary figure
#173 opened by NathanSkene - 0
Add option to keep specific gene_biotype
#164 opened by combiz - 0
Add gene_biotype filtering
#165 opened by combiz - 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 opened by NathanSkene - 0
- 0
Get 6.0.2 onto dockerhub
#169 opened by NathanSkene - 0
Add report with top marker genes for each cluster. Then we can use this to get a sense of how stable sub-cluster markers are across datasets.
#152 opened by NathanSkene - 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 opened by NathanSkene - 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 opened by NathanSkene - 0
Add option to use HPF instead of PCA throughout
#163 opened by NathanSkene - 0
Run unenriched AD, Trem2, Tsai, Grubman and the published Collonge Trem2 study through the pipeline. Analyse Trem2 + unenriched together and separately. The contrasts for Trem2 are: [Trem2 var vs CTRL] and [AD vs CTRL]. The [AD vs CTRL] can be done pooled with unenriched.
#145 opened by NathanSkene - 0
Write a report showing how [pseudobulk, glmer, bayesglm, glmer without confounds] finds gender-associated genes. Show rank of Xist + other genes found to be significantly differential using psuedobulk. Show chromosomal bias in top 100 genes.
#146 opened by NathanSkene - 0
Use the LIGER'd clusters from Beth's dataset, to integrate with LIGER against our enriched microglia data.
#147 opened by NathanSkene - 0
Why is dirichlet modelling giving tiny p-values, when the changes don't look significant at all in the bar plots, and when there are only three samples in one group?
#151 opened by NathanSkene - 0
- 0
Integrate process drops all genes. Need to fix because this means we can't run all of Amy's data through the whole of v0.5.
#140 opened by NathanSkene - 0
Does the cluster in the MS dataset, which gets called an excitatory neuron by EWCE but which expresses Plp1 (and clusters with oligos without LIGER): (a) have low EWCE probability? (b) get called doublets if doublet rate is increased?
#148 opened by NathanSkene - 0
- 1
- 1
Docker build file must be on github + setup so that it rebuilds on Dockerhub every time there are changes on github
#172 opened by NathanSkene - 1
- 0
- 0
- 1
Check the pseudobulk implementation. Get results using it. Consider implementing the
#143 opened by NathanSkene - 0
- 0
Add adaptive upper threshold for pc_mito cut-off
#157 opened by nfancy - 1
Pre-processing Seurat object is faster when FindVariableFeatures runs before NormalizeData and ScaleData
#141 opened by MahdiMoradiMarjaneh - 1
Enable the pipeline to save data in format suitable for upload to the Broad's Single Cell Portal / CellXGene
#161 opened by NathanSkene - 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 opened by NathanSkene - 1
- 1
Amend the LIGER report: (1) implement the hexogonal tSNE plots into the LIGER report, (2) get the riverplot into the LIGER report, (3) in the LIGER report, in the Clustering section, show bar plots with percentage of each cluster that comes from each group variable.
#144 opened by NathanSkene - 1
when clusters are factor some of the celltypes are coming us as number, not getting assigned any cell type.
#150 opened by nfancy - 1
HTTP error 401 when installing scFlow using install_github with token
#149 opened by MahdiMoradiMarjaneh