User: kinalimeric

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kinalimeric20
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4 years, 1 month ago
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Posts by kinalimeric

<prev • 8 results • page 1 of 1 • next >
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Complexity of gene expression in scRNA-seq data
... Dear all, I am following this tutorial which is very understandable for single-cell analysis. However, I am confused about only one concept in here which is 'complexity': https://github.com/hbctraining/scRNA-seq/blob/master/lessons/04_SC_quality_control.md So to calculate the overall complexity o ...
single-cell seurat written 19 days ago by kinalimeric20 • updated 19 days ago by rpolicastro720
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Answer: A: Is there a tutorial on pathway enrichment analysis in R without ready-made packa
... You can perform a hypergeometric test by yourself. ...
written 22 days ago by kinalimeric20
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Comment: C: SingleR for integrated scRNA-seq analysis
... But we perform integrated assay when we trying to align cell states shared across datasets. If we will use 'RNA' slot what is the point of integration? ...
written 6 weeks ago by kinalimeric20
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Comment: C: Visualize top 10 increasing peaks of the ATAC-seq data
... Thank you for your help and explanation. ...
written 4 months ago by kinalimeric20
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Comment: C: Visualize top 10 increasing peaks of the ATAC-seq data
... I have 8 samples. I performed differential binding analysis using diffbind. I want to show the peaks that change the most (top10) between those samples. ...
written 4 months ago by kinalimeric20
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Visualize top 10 increasing peaks of the ATAC-seq data
... Hi all, I want to visualize only the top ten peaks using deep tools. However, the resolution is really low if I run computeMatrix with the top 10 peaks even though I increase dpi and changing the —heatmapHeight of the heat-map. Also, I tried to run computeMatrix with all the increasing peaks then g ...
deeptools atac-seq heatmap written 4 months ago by kinalimeric20
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Comment: C: Normalization of ATAC SEQ data for the proper deeptools heatmap
... Thank you so much for your help! ...
written 5 months ago by kinalimeric20
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Normalization of ATAC SEQ data for the proper deeptools heatmap
... Hi all, I have paired-end 4 ATAC-seq data (2 replicates for 2 samples). I have done aligning using Bowtie2. I did filter MT reads and duplicates using Picard, then performed peak calling on Bam file using MACS2. Also I did differential peak analysis using deeptools and filter them by FDR<0.05 an ...
deeptools atac seq normalization written 5 months ago by kinalimeric20 • updated 5 months ago by ATpoint36k

Latest awards to kinalimeric

Voter 6 weeks ago, voted more than 100 times.
Supporter 5 months ago, voted at least 25 times.

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