Shawn_Shang

Maybe it is a good idea to add caleblareau/BuenColors

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https://github.com/caleblareau/BuenColors

how to save as a pdf

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Hi, thanks for this awesome package. I have a problem about the output html. I output the table using this function in R studio  But I want to edit...

options(ChIPseeker.downstreamDistance = 500) seems not work

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### Prerequisites + [x] Have you read [Feedback](https://guangchuangyu.github.io/chipseeker/#feedback) and follow the [guide](https://guangchuangyu.github.io/2016/07/how-to-bug-author/)? * [x] make sure your are using the latest release version * [x] read the [documents](https://guangchuangyu.github.io/chipseeker/documentation/) * [x]...

### Prerequisites + [x] Have you read [Feedback](https://guangchuangyu.github.io/chipseeker/#feedback) and follow the [guide](https://guangchuangyu.github.io/2016/07/how-to-bug-author/)? * [x] make sure your are using the latest release version * [x] read the [documents](https://guangchuangyu.github.io/chipseeker/documentation/) * [x]...

A question about general mode in logistic mode

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Hi, deal developer I have a question about general mode when traing logistic mode. In my thinking, the TF-specific mode is based on 237 TFs from REMAP. I take TF...

Hi, Dr Khan I am wondering whether I can use the fisher test in pairwise module about my species(Arabidopsis thaliana). I have made it when I use the bedtools ```...

Hi, I am running pyscenic ctx and it worked. ``` pyscenic ctx adj.csv ../related_info/cisTarget_Ath/Athaliana.genes_vs_motifs.rankings.feather --annotations_fname ../related_info/cisTarget_Ath/JASPAR_plantTFDB_Ath.tbl --expression_mtx_fname result/processed_result/CIM1d_rep2.loom --mask_dropouts --num_workers 40 --output reg.csv ``` But I have a question about...

Hi, I am new to monocle3. But I find it is hard for me to find the `logcount` result on object even after running preprocess_cds. But accroding to help document,...

Hi I noticed in line 430. when get the count of bam, you shift_width to center the read on the cut site ``` bam_array = bam.array(tss_ext, bins=bins, shift_width = -read_len/2,...

Hi, I have two question about GENIE3. First, I am wonering wether I should filter zero-count gene before calculating weights. I found some paper may use the TPM > 5...