hahia

Hello, I'm new to harmony, I feel confused about something. I have scRNA data of dataset1 and dataset2, dataset1 have the batch effect of **Platform**, dataset2 have batch effect of...

Hello, when I run the **ot_model = wot.ot.OTModel(adata, epsilon = 0.05, lambda1 = 3, lambda2 = 50, growth_iters = 5) ot_model.compute_all_transport_maps(tmap_out='tmaps/neuron_3_50_5/neuron')** there come some futurewarning 

plotGeneExpression add legend

2

Does anyone know how to add legend on plotGeneExpression when I use the split.by parameter? thank you for your help.

SaveH5Seurat error

5

Hello, when I run `SaveH5Seurat(lung.integrated, filename = "./tmp.h5Seurat")` There has an error: ``` `Error in H5File.open(filename, mode, file_create_pl, file_access_pl) : HDF5-API Errors: error #000: H5F.c in H5Fcreate(): line 444: unable...

All nan in matrix come from non negative tucker decomposition

2

Code: ``` from tensorly.decomposition import non_negative_tucker tl.set_backend('pytorch') tensor = tl.tensor(dat, device='cuda:3') facs_overall = non_negative_tucker(tensor,rank=[8,8, 8],random_state = 2337) ``` dat is    The facs_overall   Could someone provide...

Is there filter cell in the count process?

1

Hello I use velocyto to count spliced / unspliced counts on dropseq data I use the command `velocyto run -o ./loom/ -m /cluster/huanglab/hhuang/Database/RNA_velocity/rmsk/hg19/hg19_rmsk.gtf /cluster/huanglab/hhuang/project/jing/Work/2020.7.22/data_ziwei_new_alignment/CH4-LN_S1_L001_b37/star_gene_exon_tagged.bam /cluster/huanglab/hhuang/project/jing/Final_ziwei_data/20200701/Homo_sapiens.GRCh37.75.gtf` **without -b parameter** But when...

Some problem about Dropseq data

1

Hello, this is a amazing tool. I have some problems when I analysis Dropseq data. Maybe you have some expriences can help me solve these problems 1. After the pipeline...

why min_shadow is greater than mean_shadow and median_shadow?

1


unused argument when create_kegg_db

9


Hello, I'm new to PAGA connectivity score. I don't understand how paga connectivity score is calculated.  Can anyone explain what's mean of random assignment of edges? And if the...