User: zhao03

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zhao0330
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1 year, 10 months ago
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Posts by zhao03

<prev • 44 results • page 1 of 5 • next >
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how to find variation gene in specific state in monocle
... Hi, i used monocle to find out one branch_point with three branchs, and i want to figure out variation gene in branche one , how can i get the result , thank you ...
R rna-seq written 28 days ago by zhao0330
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(Closed) TF motif predicttion
... hi, i have a sequence about 2000kb, how can i identify the motif or TF binding site on this sequence? thanks a lot! ...
chip-seq written 3 months ago by zhao0330 • updated 6 weeks ago by Biostar ♦♦ 20
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how can i evaluate the different between two samples of distribution of peaks in the genome of chip-seq
... Hi i showed the heatmap of TSS region used Deeptools, and found there was a different between two samples, however, how can i get a statistic(p value or fold change?) to indicate the difference? thank you for your help! ![enter image description here][1] [1]: https://deeptools.readthedocs.io/en/ ...
chip-seq written 3 months ago by zhao0330
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why the different peaks by HINT-ATAC all under the zero line and motif Activity Score are negativate
... Hi, i used HINT-ATAC to find motif of S3 and S5 sample, and then, i used rgt-hint differential to discover the different motif between S3 and S5, however, the result figure shows all the motif Activity Score are negativate. how can i understand? thank you ![enter image description here][1] [1]: ...
chip-seq written 5 months ago by zhao0330
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"Idents" can not be use in seurat
... Hi, three kind of clusters i discoverd by different dim, now i want to use result of res.0.4 to plot UMAP. However, there is error when i used the command as fllowing: Idents(D3_APLNR)<-"res.0.4" Error in UseMethod(generic = "Idents<-", object = object) : no applicable method for 'Id ...
software error rna-seq written 6 months ago by zhao0330 • updated 6 months ago by jomo018610
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Got the negative value when used ComBat to Adjust batch effects
... Hi, i used combat to remove the batch bais, however, there are some negative numbers in the result matrix. what is the means of those negative number, can i use this matrix to find the different gene? i inputted FPKM for running combat. the command is combat_edata1 = ComBat(dat=edata, batch ...
software error R written 6 months ago by zhao0330 • updated 3 months ago by ATpoint44k
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Answer: A: removing batch effects using ComBat and SVA
... Hi, i also used combat to remove the batch bais, however, there are some negative numbers in the result matrix. what is the means of those negative number, can i use this matrix to find the different gene? i inputted FPKM for running combat. ...
written 6 months ago by zhao0330
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are there some tools or software can find the different peak of ATAC-seq
... Hi i got the ATAC-seq peaks by MACS2 cellpeak, How can i find the different peak between case and cotrol? thank you! ...
genome chip-seq written 6 months ago by zhao0330 • updated 6 months ago by Rory Stark900
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what is the result files of MACS2 bdgdiff
... hi, i used to find the difference peak of ATAC-seq by MACS2 bdgdiff, but i cant undersand what the means of the fourth column in results, the command is macs2 bdgdiff --t1 S5_treat_pileup.bdg \ --c1 S5_control_lambda.bdg \ --t2 S3_NT_treat_pileup.bdg \ ...
chip-seq atca-seq written 6 months ago by zhao0330
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what is the mean of "%" in DAVID Gene-annotation enrichment analysis
... Hi, when i ran gene enrichment in DAVID , i got the result like this, however , i don't understand the column of "%". Term Count % PValue List Total Pop Hits Pop Total GO:0070062~extracellular exosome 1179 39.93902439 2.15E-295 2911 2811 18224 thank you for your help!~ ...
gene software error written 9 months ago by zhao0330 • updated 9 months ago by Jean-Karim Heriche24k

Latest awards to zhao03

Popular Question 3 months ago, created a question with more than 1,000 views. For Where can I download the length of short and long arms for each chromosome
Popular Question 3 months ago, created a question with more than 1,000 views. For i can't find the SRR sample on NCBI FTP, such as SRR018260
Popular Question 6 months ago, created a question with more than 1,000 views. For i can't find the SRR sample on NCBI FTP, such as SRR018260

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