User: Folder40g

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Folder40g120
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Posts by Folder40g

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Measure distance between genesets
... I have several genesets from differential expression analyses (30 to 400 genes at each geneset). These genesets come from performing expression analysis comparing different cell types, I would like to see whether those genesets from same cell type are more similar than those from other cell types. ...
genesets distance written 6 months ago by Folder40g120
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3 prime RNA sequencing depth fro DEG analyses (Quantseq)
... Hi Is there any paper were people have analyzed the optimal number of reads for differential expression analyses using quantseq 3' sequencing. So far I've only been able to find papers were authors compared differences between "standard" RNA sequencing vs 3' sequencing, normally starting from 10 mi ...
quantseq written 10 months ago by Folder40g120
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Weighted rank list comparison
... Hi, I'm interested gene ranked list comparison, these lists come from a DEG analysis (log2 ordered). Normally I would select DEG as gene sets (up or down) from one list and through GSEA I would test for enrichment against a the other pre-ranked list. In this case I would like to compare two ful ...
rank comparison written 12 months ago by Folder40g120
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TCGA expression data (TPM)
... I'm using a software that requieres either TPM or raw counts at gene level. So I downloaded this data set from Xena browser: https://xenabrowser.net/datapages/?dataset=TCGA.SKCM.sampleMap%2FHiSeqV2&host=https%3A%2F%2Ftcga.xenahubs.net This matrix seems to be the log2(RSEM output + 1) Am I wro ...
tcgabiolinks tcga tpm expression written 21 months ago by Folder40g120 • updated 16 months ago by Israel Barrantes790
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TCGA purity data
... Hi I know that Cosmics offers a file with the purity for each tumor sample but no BAF or LogR, but I'm interested in running ascat on some TCGA samples to obtain Germline/Tumor BAF and LogR for a downstream analysis. Do you know if there is any database with this information available? I've not fo ...
tcga ascat purity written 23 months ago by Folder40g120
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rsem matrix to DESeq2
... I know that I can pass the gene-level rsem matrix to limma and work with it. But can I use it in DESeq? I've a rsem matrix from firebrowse, gene-level ~20000 rows. DESeq requires raw counts, and as I only have the matrix with samples/gene I can't use tximport(). Thanks ...
rsem written 23 months ago by Folder40g120 • updated 23 months ago by Kevin Blighe60k
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Comment: C: Question: Unmapped reads at TCGA bam files
... Yes, it seems thats what is happening. A "bug" from STAR aligner. ...
written 2.1 years ago by Folder40g120
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Question: Unmapped reads at TCGA bam files
... I haven't use samtools for a while and now I've some files from TCGA from which I'm checking the reads. I'm trying to see if there are any unmapped sequences at TCGA bam files: `samtools view -f 4 file_gdc_realn_rehead.bam` and I get this `UNC-SN:197:C0XX:4:204:155:805 69 chr1 14496 0 * = 14496 0 A ...
tcga bam written 2.1 years ago by Folder40g120 • updated 2.1 years ago by toralmanvar840
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Comment: C: Meaning letters in TCGA sample barcode field
... Thanks I was trying to get that image. ...
written 2.1 years ago by Folder40g120
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Meaning letters in TCGA sample barcode field
... Hi, I've a doubt for which I've no answer. The fourth field of the TCGA barcode contains the information about the sample, either primary tumor, metastatic, etc For instance `TCGA-93-A4JP-01A-11H-A24S-13`, this is a primary tumor, but what does the A next to the 02 means? Sometimes I've sen other ...
barcode tcga written 2.1 years ago by Folder40g120 • updated 2.1 years ago by Kevin Blighe60k

Latest awards to Folder40g

Popular Question 12 months ago, created a question with more than 1,000 views. For Skip orientation RF
Good Question 21 months ago, asked a question that was upvoted at least 5 times. For Bimodal GC content
Popular Question 21 months ago, created a question with more than 1,000 views. For Skip orientation RF
Popular Question 21 months ago, created a question with more than 1,000 views. For rsem matrix to DESeq2
Popular Question 21 months ago, created a question with more than 1,000 views. For Raw counts TCGA Firebrowse
Popular Question 21 months ago, created a question with more than 1,000 views. For Gene Symbol to KEGG
Popular Question 21 months ago, created a question with more than 1,000 views. For Adapters SureSelect QXT
Popular Question 21 months ago, created a question with more than 1,000 views. For Meaning letters in TCGA sample barcode field
Popular Question 22 months ago, created a question with more than 1,000 views. For Skip orientation RF
Popular Question 22 months ago, created a question with more than 1,000 views. For Skip orientation RF
Student 2.4 years ago, asked a question with at least 3 up-votes. For Raw counts TCGA Firebrowse
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Skip orientation RF
Popular Question 3.0 years ago, created a question with more than 1,000 views. For Bimodal GC content
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Bimodal GC content
Appreciated 3.6 years ago, created a post with more than 5 votes. For Bimodal GC content
Student 4.3 years ago, asked a question with at least 3 up-votes. For Bimodal GC content

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