User: thomasterTW

gravatar for thomasterTW
thomasterTW20
Reputation:
20
Status:
New User
Location:
RIMLS, Nijmegen, The Netherlands
Last seen:
2 years, 10 months ago
Joined:
3 years, 3 months ago
Email:
t**************@gmail.com

Posts by thomasterTW

<prev • 10 results • page 1 of 1 • next >
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New isoform discovery with paired end reads across different exons
... I am trying to figure out which isoform of a protein is expressed in my cells. I have reads in exons suggesting that either multiple isoforms are expressed, or a yet undiscovered isoform is expressed. To test this I need a tool that uses paired end reads across different exons in order to 'link' tho ...
paired end rna-seq isoform written 2.9 years ago by thomasterTW20 • updated 2.9 years ago by EagleEye6.3k
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Comment: C: Pheatmap cluster number labels
... I still can't get it to work :( This it the output of pheatmap: > res $tree_row Call: hclust(d = d, method = method) Cluster method : complete Distance : euclidean Number of objects: 6445 $tree_col [1] NA $kmeans [1] NA $gtable ...
written 2.9 years ago by thomasterTW20
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Comment: C: Pheatmap cluster number labels
... I already fixed the problem. Should be `res2<-matrix[c(res$tree_row[["order"]]),]` ...
written 2.9 years ago by thomasterTW20
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Comment: C: Pheatmap cluster number labels
... Thanks! That's what I need. However, when I try this method I get an error. res2<-matrix[c(res$tree_row[["order"])]] Error in `[.data.frame`(matrix, c(res$tree_row[["order"]])) : undefined columns selected ...
written 2.9 years ago by thomasterTW20
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Pheatmap cluster number labels
... My question is very simple. When I use the clustering option in pheatmap, for example: res<-pheatmap(matrix, scale="row", cluster_cols=FALSE, show_rownames=FALSE, cutree_rows=8, color=colorRampPalette(c("red","black","green"))(50), cellwidth=30, cellheight=0.4, main="C2C7_Differential_Gene_E ...
pheatmap rna-seq clustering written 2.9 years ago by thomasterTW20 • updated 17 months ago by sisterdot20
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Comment: C: Combining RNA seq and H3K27ac ChIP seq data
... I find this one very interesting, though I'm not sure how to use it. It says it will combine ChIP-seq of TF or chromatin regulators with cuffdiff results. However it seems that all functions in this software are based on transcription factors and their target detection. In their tutorials and readme ...
written 2.9 years ago by thomasterTW20
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Combining RNA seq and H3K27ac ChIP seq data
... I have 2 lists of comparisons between 3 conditions: (1->2 and 2->3) - List of differential gene expression (genes) (RNA seq data analyzed with DESeq2) - List of differential H3K27ac binding (peaks) (ChIP seq data analyzed with MAnorm) I want to find correlation between gene expression dynam ...
h3k27ac chip-seq deseq rna-seq manorm written 2.9 years ago by thomasterTW20 • updated 2.9 years ago by Ming Tang2.5k
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Looking for the best way to annotate histone modicitation marks to genes.
... I want to include differential binding of H3K27ac (ChIP-Seq) near genes in my differential gene expression (RNA-seq) analysis. The aim of this analysis is to see the expression dynamics in a cellline between 3 time points (proliferating (day 0) and differentiation (day 1.5 and 3)). I want to see for ...
htseq-count chip-seq star rna-seq readcounts written 2.9 years ago by thomasterTW20 • updated 2.9 years ago by SP250
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Comment: C: Remove rows based on duplicates in one column
... Thanks! This works very well ...
written 3.2 years ago by thomasterTW20 • updated 8 months ago by RamRS21k
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Remove rows based on duplicates in one column
... I'm doing RNAseq analysis to determine differential expression patterns. After running a custom R script to determine the cut off between expressed and unexpressed genes (kernel density plot), I get a list with 4 columns. Ensembl ID Short gene name Locus 10Log FP ...
duplicates rna-seq written 3.3 years ago by thomasterTW20 • updated 8 months ago by RamRS21k

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