User: friasoler

gravatar for friasoler
friasoler20
Reputation:
20
Status:
New User
Location:
Germany
Last seen:
11 months ago
Joined:
5 years, 5 months ago
Email:
f********@gmail.com

Posts by friasoler

<prev • 39 results • page 1 of 4 • next >
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RPKM and TPM calculation
... Dear colleagues I have used three different ways to calculate RPKM from my data, one from a colleague, from a post in internet and my own way and we three have different outputs, obviously just one is the right one; but can you do your own calculation and shared with me? What would be the TPM you w ...
rpkm rna-seq written 11 months ago by friasoler20 • updated 11 months ago by kristoffer.vittingseerup3.3k
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Comment: C: Nested data frames in a list
... Many thanks! It work very well. At the end I would like to filter out all genes with less than 3-10 reads to conduct differential gene expression analysis. I'm aiming to rebuild 'cm' having "zeros" in the rows which total-sum<3 reads by tissue (B: brain...etc). ...
written 11 months ago by friasoler20
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Comment: C: Nested data frames in a list
... Thanks Fabio, here an example of my CM matrix: B1 B2 B3 F1 F2 F3 I2 I3 I4 L1 L2 L3 M4 M5 M6 S1 S2 S3 OOENG00001 4 3 11 6 5 27 2691 2665 3238 2960 1893 2329 0 0 1 1 10 10 OOENG00002 12646 11932 17689 45610 55731 44342 451 474 437 1597 2077 4722 298 220 272 9769 11618 13528 OOE ...
written 11 months ago by friasoler20
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Nested data frames in a list
... Dear colleagues I'm trying to create a list of data frames from an original matrix. Each new data frame should have a new column with a row-sum that will be used to subset the new data frames accordingly. The point is I'm unable to get the desired data frame structure with multiple columns, I just ...
R list dataframe written 11 months ago by friasoler20 • updated 11 months ago by Fabio Marroni2.5k
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Aggregate data frame using function with a logical criterion
... I would like to detect which of the elements in the first column (gene) have an ambiguous value in the second column (log2 fold.change). Note that "Golgi integral membrane protein 4-like" has different sign of log2 fold change, but "protein HEG homolog 1" no. I would like to have a final data frame ...
R aggregate written 14 months ago by friasoler20 • updated 14 months ago by Biostar ♦♦ 20
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How to use simultaneously long and short reads to assemble de novo a transcriptome?
... Dear colleagues Thanks in advance for your help I would like to assemble, de novo, a transcriptome from which I have two kind of data: 1) long reads (Illumina Roche GS FLX System, single-end reads ~400bp) 2) Short reads illumina ~40bp. I have used already the long reads for the assembly but the re ...
hybrid reads transcriptome de novo rna-seq written 21 months ago by friasoler20 • updated 21 months ago by Antonio R. Franco4.5k
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coloring a plot
... Hello everyone! I would like to have a plot with some points in different colors; but I get an empty plot. Could someone help me? a=data.frame(b= c(1:26), c=rnorm(26), d=paste(letters[1:26])) e=data.frame(a$d[3:15]) colnames(e)=c("d1") #variant 1 plot(a$b, a$c, col= (if (a$b<5) { ...
conditional plot colors R plot written 3.2 years ago by friasoler20
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Comment: C: Reshape tabular data frame to wide format
... Thanks a lot Healey! ...
written 3.2 years ago by friasoler20
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Comment: C: Reshape tabular data frame to wide format
... It has sense...the columns are loci...each one with two alleles by sample ... Thanks ...
written 3.2 years ago by friasoler20
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Reshape tabular data frame to wide format
... Hello everyone! I would appreciate some help with this data frame 'df': # df Marker Sample allele FlaHDF11 CP26 h FlaHDF11 CP26 a FlaHDF12 CP26 e FlaHDF12 CP26 f FlaHDF11 CP27 g FlaHDF11 CP27 h FlaHDF12 CP27 t FlaHDF12 CP27 z I would like something tl ...
R written 3.2 years ago by friasoler20 • updated 3.2 years ago by cmdcolin1.3k

Latest awards to friasoler

Great Question 21 months ago, created a question with more than 5,000 views. For read FASTA file in R, including description information
Epic Question 21 months ago, created a question with more than 10,000 views. For ggplot2 graphs are empty
Popular Question 21 months ago, created a question with more than 1,000 views. For read FASTA file in R, including description information
Popular Question 21 months ago, created a question with more than 1,000 views. For To compare gene expression profiles.
Great Question 3.1 years ago, created a question with more than 5,000 views. For ggplot2 graphs are empty
Popular Question 3.1 years ago, created a question with more than 1,000 views. For read FASTA file in R, including description information
Popular Question 3.1 years ago, created a question with more than 1,000 views. For To compare gene expression profiles.
Popular Question 3.1 years ago, created a question with more than 1,000 views. For IGV no visualization of BAM files
Popular Question 3.1 years ago, created a question with more than 1,000 views. For How to merge metabolic or regulatory pathways from a list of genes
Popular Question 3.1 years ago, created a question with more than 1,000 views. For Help with-- Cytoscape- ClueGO- Bingo
Popular Question 3.1 years ago, created a question with more than 1,000 views. For read FASTA file in R, including description information
Popular Question 3.6 years ago, created a question with more than 1,000 views. For read FASTA file in R, including description information
Popular Question 3.6 years ago, created a question with more than 1,000 views. For ggplot2 graphs are empty

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