Zhen Zuo

gunzip -c chr*.fa.masked > hg19.fa

5

Hello, When I run ``` gunzip -c chr*.fa.masked > hg19.fa ``` in [CENTIPEDE.tutorial](https://slowkow.github.io/CENTIPEDE.tutorial/) in Genomic sequence Section, I got the following error ``` gzip: chr10.fa.masked: not in gzip format gzip:...

Hi, I got the following error when trying to install velocyto: (mypython3) -bash-4.2$ pip install -e . Obtaining file:///storage/chen/home/zz4/velocyto.py Requirement already satisfied: numpy in /storage/singlecell/zz4/miniconda3/envs/mypython3/lib/python3.8/site-packages (from velocyto==0.17.16) (1.21.0) Requirement already...

R kernel keeps dying when running mcell_mc_from_coclust_balanced()

7

*** caught segfault *** address 0x558cbaa2fc00, cause 'memory not mapped' Traceback: 1: tgs_graph_cover(edges, min_mc_size, cooling = tgs_clust_cool, burn_in = tgs_clust_burn) 2: mcell_mc_from_coclust_balanced(coc_id = "retina_coc500", mat_id = "retina", mc_id = "retina_mc",...

plot_network_graph() only plot target genes

1

Hi, The dimension of `seurat_object@grn@networks$glm_network@graphs$umap_graph` is the same as number of target genes saved in `seurat_object@grn@networks$glm_network`. As a result, only TFs that are also target genes were plotted. Is this...

### Description of the bug Line 240 at https://github.com/nf-core/epitopeprediction/blob/master/bin/epaa.py is `isSynonymous = a_mut_type == "synonymous_variant"`. This not work for cases such as `splice_region_variant&synonymous_variant`. It can be `isSynonymous = "synonymous_variant" in...

BioMart request declined

6

### Description of feature Hi, Thank you for developing epitopeprediction! I got error when running [](https://github.com/nf-core/epitopeprediction/blob/master/bin/epaa.py) at line 1133 `transcriptProteinTable = ma.get_protein_ids_from_transcripts(transcripts, type=EIdentifierTypes.ENSEMBL)`. If the input variant list is too...