User: eggrandio

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eggrandio40
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Posts by eggrandio

<prev • 15 results • page 1 of 2 • next >
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Comment: C: Biomart query returns NA when searching for entrez_id, while manual search works
... Thanks for your reply! A while ago I tested both ways (for different queries, related with GOs) and it seemed that ensembl through biomaRt was more complete, but in this case it looks like the contrary. I guess it depends on the query... I wish there was a unified database. I might have to write ...
written 4 weeks ago by eggrandio40
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Comment: C: Biomart query returns NA when searching for entrez_id, while manual search works
... But when I look it up in the NCBI website, it returns entrez_id 824648, and once [there][1], I can find the NM IDs: NM_001339700.1 and NM_115340.3 corresponding to those two refseq_peptide entries. I guess it could be because the database at ensembl is not updated? I find it weird, as it looks like ...
written 4 weeks ago by eggrandio40
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Biomart query returns NA when searching for entrez_id, while manual search works
... Hi, I am using biomart to convert gene IDs into entrezid accessions. I am working with arabidopsis genes, and sometimes, the query will not return an entrezid. However, when I look up that gene in the ensembl webpage, I am able to find the correspondence. Maybe I am using the wrong Mart/Dataset? H ...
R biomart arabidopsis refseq written 5 weeks ago by eggrandio40 • updated 4 weeks ago by Kevin Blighe61k
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Comment: C: Clustering differentially expressed genes in response to multiple treatments (us
... Is that not allowed? I can remove my post here or there. I don´t know which forum would be best for this type of question. ...
written 9 weeks ago by eggrandio40
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Clustering differentially expressed genes in response to multiple treatments (using edgeR)
... Hello, I am analyzing RNA-seq data of arabidopsis samples in response to three treatments (let's call them WT, RT and DT). These treatments have some components in common, so I want to find genes that respond specifically to the unique components in each treatment. In summary, I have performed th ...
complexheatmap rna-seq clustering edger heatmap written 9 weeks ago by eggrandio40
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Using block annotation with predefined dendrogram
... Hi, I am using ComplexHeatmaps to represent a heatmap data, but I want to cluster the columns by another value, so I am inputting a predefined dendrogram. I would like to include a Block Annotation to be able to write inside each block. I am giving a pre-clustered object to cluster_columns and wh ...
R dendrogram clustering complexheatmap written 10 weeks ago by eggrandio40
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Comment: C: Extract coordinates of upstream region up to closest coding region in R
... Yes, that is my problem. Maybe it's not so common in human genome, but I can find examples very easily in Arabidopsis. ...
written 16 months ago by eggrandio40
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Comment: C: Extract coordinates of upstream region up to closest coding region in R
... Thanks for your reply. I know how to remove any coding region from the upstream regions, but the problem is that I only want the region from the transcription start site up to the closest upstream gene, and nothing else upstream. I would need some way to "anchor" the feature to the TSS but I do not ...
written 16 months ago by eggrandio40
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Extract coordinates of upstream region up to closest coding region in R
... Hi, I am doing an analysis of transcription factor binding and I need to retrieve the promoter region of all the genes in the genome. I can obtain 2kb upstream easily from a TxDB object by: library(GenomicRanges) library(TxDb.Athaliana.BioMart.plantsmart28) gnflanks = flank(genes(TxDb. ...
genome R sequence written 16 months ago by eggrandio40 • updated 16 months ago by Alex Reynolds30k
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Comment: C: Reorder heatmap rows in a dataset with missing values
... Hi, I was using pheatmap because it was recommended by a lab mate, but I have no preference, I can use heatmap.2 too to generate my heatmap, but still do not get the expected results. heatmap.2(mat, Colv="none",Rowv = as.dendrogram(cluster),breaks = mat_breaks,col = brewer.pal(n = 10, name = " ...
written 2.1 years ago by eggrandio40

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Popular Question 16 months ago, created a question with more than 1,000 views. For Reorder heatmap rows in a dataset with missing values

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