jiawen wang

np.sum(auc_mtx, axis=0).sort_values(): SRY(+) | 12.34071 ZIC5(+) | 45.86162 NEUROG1(+) | 70.31318 KLF14(+) | 87.62278 CUX2(+) | 93.68485 ZNF302(+) | 114.3998 PKNOX2(+) | 121.1167 FOXA2(+) | 129.1522 BHLHE22(+) | 147.101 DLX6(+)...

np.sum(auc_mtx, axis=1).sort_values(): (it's too long to show the full dataset) S3PA_TCACAAGAGCTTCGCG | 12.57858 S3AO_CCAATCCGTCAAGCGA | 12.79109 S3AO_ACGAGCCCAGAGTGTG | 13.03914 S3AO_GATGCTAAGCTGTCTA | 13.05284 S3PA_AGCAGCCCACCTATCC | 13.12916 S3PA_AACCATGCAAGGACAC | 13.22664 S3AO_ACTGATGTCATCACCC |...

@taoliu > @crazyhottommy @igordot Yes. With -f BAMPE on, MACS2 read the left mate and the insertion length information from BAM file, and discard right mate. With -f BAM, MACS2...

You can use HMMRATAC instead now, which is a substitution of MACS2 spcific designed to ATACseq. It is developed by Tao Liu too.

I have checked some chunk of code of tangram such as mapping utils.py. I am confused about the algorithm to compute prior density based on rna count. Because in the...

Besides, I am not sure if tangram's cluster expression works on scaled data. probably it works, if the single cell data and spatial transcriptome both use the scaled data.

Dada2 only supports illumina Hiseq and Miseq platfrom now, and must make some modifications to process X-ten and Novaseq data, is it ? @benjjneb

@benjjneb Most of the companies are equipped with X-ten and Novaseq here for it's high-throughput, speed and lower sequencing costs. So this issue will emerge more and more later on....

My adata stores scaled data, and adata.raw stores raw counts, could you give me an example on how to test it using negative binomial noise models ? adata.raw only contains...

I met the same error