bxhu
bxhu
Hello, Enformer looks great to predict gene expression. Is there a piprline to run Enformer? ` I have another question. I have many DNA sequences with different length. Now I...
hello, I use this command to set the font: p("Cis-regulatory elements are regions of non-coding DNA controlling transcription regulation by binding to transcription factors"` , style = "font-family: 'Arial'; font-si10pt"`)...
Hello, would you like to tell me that hicConvertFormat can convert HiC-Pro **iced matrix** to cool or other formats? hicConvertFormat -m fastq_100000_iced.matrix --bedFileHicpro ${bed} --resolutions 100000 --inputFormat hicpro --outputFormat cool...
hello, I have a question on pearson correlation matrix (https://hicexplorer.readthedocs.io/en/latest/content/example_usage.html#a-b-compartment-analysis): how to you calculate the correlation for bewteen 2 loci (such as 100kb) per chromosome? Becasue each locus has only...
Hello, I have run MACS3 to call peaks from IP and input files, and obtained the peaks and related fold enrichment. **Peaks** are filtered based on fold enrichment>5 and q...
Hello, I have paired-end MeRIP-seq and input RNA-seq. the input files are bam files generated by Hisat2. When I ran MACS3 with -f BAM, it works. However, when setting -f...
Hello, I am trying to install chromVAR, But I got the folllowing errors: 1: In i.p(...) : installation of package ‘DirichletMultinomial’ had non-zero exit status 2: In i.p(...) : installation...
Hi, I first installed Docker, and installed Anaconda3 in Win10. I try to install HiGlass in the conda using `pip install higlass-manage`. But I got this error: Using cached pysam-0.15.4.tar.gz...
hello, Thanks for developing ABC model which is a great algorithm predicting enhancer target genes. I just have ChIP-seq and ATAC-seq bigwig files. For calling peak, I can convert these...
Hi, I want to get the coordinates of input file by extending 1000000bp up/downstream of TSS: cat input.csv | awk 'NR>1{print $1"\t"$5"\t"$6}' | bedtools window -b stdin -a genes.bed -w...