User: mickey_95

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mickey_9530
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Posts by mickey_95

<prev • 34 results • page 1 of 4 • next >
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Comment: C: Size factors upon collapsing replicates in RNA-seq analysis
... True! Argh I was overcomplicating things. Thanks a lot! ...
written 23 days ago by mickey_9530
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Size factors upon collapsing replicates in RNA-seq analysis
... Hello, I have a time-course RNA-seq dataset with two biological replicates per condition. To identify genes that are DE throughout time, I used DESeq2 and an LRT test. Now, I would like to identify group of genes that behave similarly throughout time using DEGreport::degPatterns(). As input I use s ...
R deseq2 rna-seq written 23 days ago by mickey_9530
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Comment: C: Functional enrichment analysis of bacteria
... Cool, I hadn't heard of GSEA-pro, will give it a try. Thanks!! ...
written 9 weeks ago by mickey_9530
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Functional enrichment analysis of bacteria
... Hello, I have gene lists from an RNA-seq experiment from E.coli bacteria. So far, I have only worked with model organisms, which are supported by biomaRt, so conversion of gene IDs and functional enrichment analysis within R was easy. Now that I am working with a bacterial dataset for which there i ...
R bacteria david go enrichment clusterprofiler written 3 months ago by mickey_9530 • updated 10 weeks ago by damki10
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Comment: C: RNA-seq expression patterns
... This sounds very reasonable, thanks! I just discovered the degPatterns() function from the DEGreport package: It clusters genes according to their pattern throughout time; as input I used DE genes resulting from LRT in DESeq2 ...
written 3 months ago by mickey_9530
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Comment: C: RNA-seq expression patterns
... Wow, thanks for the super quick and helpful reply!! Yes, I have already generated heatmaps and there are distinct groups/patterns, but I was wondering if that is the best approach for this. I was not aware of LRT, so far I've only used the default Wald test in DESeq2. Thanks a lot for pointing this ...
written 3 months ago by mickey_9530
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RNA-seq expression patterns
... Hi, I have an time-course RNA-seq data set with 8 different time points. I am trying to find expression patterns in the data - clusters of genes that change in similar ways throughout the experimental conditions. I guess one option would be to do pair-wise comparisons in DESeq2 by specifying the c ...
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Finding overlaps between GRanges objects
... Hi, I have a list of ChIP-seq peak regions and I am curious about those peaks overlapping annotated promoter regions. Inspired by this tutorial http://cbdm-01.zdv.uni-mainz.de/~jibnsale/teaching/chip-seq_exercises.html#functional-annotation-of-chip-seq-peaks (more specifically, sections 5.3 and 5 ...
peak iranges promoter chip-seq granges written 3 months ago by mickey_9530 • updated 3 months ago by Jimbou820
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Comment: C: TSS metaprofile using Deeptools
... Here are the first lines of the gtf file: chr1 ensembl_havana gene 5588466 5606131 . + . gene_id "ENSMUSG00000025905"; gene_version "14"; gene_name "Oprk1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; chr1 ensembl_havana gene 6206197 6276648 . + . gene_id "ENSMUSG0000002590 ...
written 7 months ago by mickey_9530
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TSS metaprofile using Deeptools
... Hi, I am trying to use Deeptools' computeMatrix and plotHeatmap functions to create TSS-centered metaprofiles over all genes. Ultimately, I would like to apply some additional filters, e.g. protein-coding, non-overlapping TSSs, above a certain size. But for an initial trial, I decided to just filte ...
gtf deeptools computematrix metaprofile written 7 months ago by mickey_9530 • updated 7 months ago by zhuobaowen10

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Popular Question 3 months ago, created a question with more than 1,000 views. For ATAC-seq peak calling

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