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README.md

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 **Python**: [Conda on O2](python/conda.md)
 
-**RC**: [Connection to HPC](rc/connection-to-hpc.md) * [Keep command alive](rc/keepalive.md) * [IPython notebook](rc/ipython-notebook-on-O2.md) * [Manage files](rc/manage-files.md) * [O2 tips](rc/O2-tips.md) * [Scheduler](rc/scheduler.md) * [Jupyter notebooks](rc/jupyter_notebooks.md) * [tmux tips](rc/tmux.md) * [FAS virtual desktops](rc/openondemand.md)*[Arrays in Slurm](rc/arrays_in_slurm.md)
+**RC**: [Connection to HPC](rc/connection-to-hpc.md) * [Keep command alive](rc/keepalive.md) * [IPython notebook](rc/ipython-notebook-on-O2.md) * [Manage files](rc/manage-files.md) * [O2 tips](rc/O2-tips.md) * [Scheduler](rc/scheduler.md) * [Jupyter notebooks](rc/jupyter_notebooks.md) * [tmux tips](rc/tmux.md) * [FAS virtual desktops](rc/openondemand.md)*[Arrays in Slurm](rc/arrays_in_slurm.md)*[Common O2 portal Issues](O2_portal_errors.md)
 
 **[Single Cell RNA-seq](scrnaseq/README.md):** [Bcbio indrops3](https://bcbio-nextgen.readthedocs.io/en/latest/contents/single_cell.html#workflow) * [Rstudio docker](scrnaseq/rstudio_sc_docker.md) * [Saturation](scrnaseq/saturation_qc.md) * [Clustering analysis in Seurat](scrnaseq/seurat_clustering_analysis.md) * [Seurat markers](scrnaseq/seurat_markers.md) * [Single Cell conda](scrnaseq/Single-Cell-conda.md) * [Cell types](scrnaseq/tinyatlas.md) * [Tools](https://github.com/seandavi/awesome-single-cell) * [Tutorials](scrnaseq/tutorials.md) * [Bibliography](scrnaseq/bibliography.md) * [Velocity](scrnaseq/velocity.md) * [Doublets](scrnaseq/doublets.md) * [Zinbwaver](scrnaseq/zinbwaver.md) * [pseudobulk DESeq2](https://github.com/hbctraining/scRNA-seq_online/blob/master/lessons/pseudobulk_DESeq2_scrnaseq.md) * [pseudobulk edgeR](scrnaseq/pseudobulkDE_edgeR.md) * [CITE-seq](scrnaseq/cite_seq.md) * [Library structures](https://teichlab.github.io/scg_lib_structs/) * [Seurat to 10X counts](scrnaseq/write10Xcounts.md) * [Azimuth](https://azimuth.hubmapconsortium.org/) * [Running Cell Ranger O2](scrnaseq/CellRanger.md) * [Cluster annotation tutorial](https://www.nature.com/articles/s41596-021-00534-0) * [Diff composition analysis](https://github.com/theislab/scCODA) * [OSCA](https://bioconductor.org/books/release/OSCA/) * [upstream TF with pySCENIC](https://github.com/hbc/knowledgebase/blob/master/scrnaseq/pySCENIC.md) * [SC article list for beginners](https://threadreaderapp.com/thread/1577714756047278080.html) * [demuxafy (includes demultiplexing, background and doublet detection tools](https://github.com/hbc/knowledgebase/blob/master/scrnaseq/Demuxafy_HowTo.md) * [Lymphocyte Antigen Receptor Transcripts and Clustering](https://github.com/hbc/knowledgebase/blob/master/scrnaseq/Thoughts_on_lymphocyte_Antigen_Receptor_transcripts_in_sc_RNA_Seq_analyses.md) * [DoubletFinder](https://github.com/hbc/knowledgebase/blob/master/scrnaseq/running_doubletfinder.md) * [Running Mast](https://github.com/hbc/knowledgebase/blob/master/scrnaseq/running_MAST.md) * [Publication Quality UMAPs](https://github.com/hbc/knowledgebase/blob/master/scrnaseq/pub_quality_umaps.md)