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8 results • Page
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Tutorial:
Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq
Survival
TCGA
updated 3 days ago by
Ram
39k • written 7.8 years ago by
TriS
★ 4.6k
83
votes
34
replies
16k
views
22 follow
Tutorial:
Enrichment Analysis, Clustering and Scoring with pathfindR
enrichment
R
pathway
active-subnetwork
updated 1 day ago by
adelheidkratzer
• 0 • written 4.9 years ago by
egeulgen
★ 1.3k
59
votes
15
replies
12k
views
Tutorial:
Which human reference genome should I use?
assembly
genome
alignment
updated 3 days ago by
Ram
39k • written 4.6 years ago by
finswimmer
16k
3
votes
4
replies
4.0k
views
Tutorial:
gencore: a tool to reduce sequencing noises by generating consensus reads
consensus
OpenGene
sequencing-noise
updated 5 days ago by
Ram
39k • written 5.1 years ago by
chen
★ 2.4k
3
votes
4
replies
3.3k
views
Tutorial:
Gene Set Enrichment Analysis on T-BioInfo
gene
RNA-Seq
updated 2 days ago by
Ram
39k • written 4.6 years ago by
elia.brodsky
▴ 340
1
vote
4
replies
3.0k
views
Tutorial:
Applying machine learning to NGS transcriptomic data
next-gen
RNA-Seq
updated 5 days ago by
Ram
39k • written 5.0 years ago by
elia.brodsky
▴ 340
2
votes
0
replies
1.2k
views
Tutorial:
Principal Component Analysis (PCA ON T-BIOINFO)
RNA-Seq
next-gen
updated 4 days ago by
Ram
39k • written 4.9 years ago by
elia.brodsky
▴ 340
0
votes
0
replies
1.1k
views
Tutorial:
In the cloud - Guide to running VerifyBamID to estimate DNA sample contamination
sequence
cloud
dna
sequencing
updated 3 days ago by
Ram
39k • written 4.8 years ago by
corlinp
• 0
8 results • Page
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Recent Votes
Answer: extract all fasta sequence from db v5
Does the RNAseq data normal if the TPM value 3rd Qutile expression is near 10, but the Max expression are near 20,000
Comment: Does the RNAseq data normal if the TPM value 3rd Qutile expression is near 10, b
Answer: Does the RNAseq data normal if the TPM value 3rd Qutile expression is near 10, b
A: extract dendrogram cluster from pheatmap
Answer: Counting intronic reads in bulk RNA-seq
Answer: IGV displays genomic coordinates in a 1-based system or 0-based?
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Recent Replies
Comment: DEgs RNAseq
by
Juan
• 0
Dear Delaney Sullivan, thanks, finlly I did my analisys
Answer: ScRNA data
by
Dr William Klubinski
▴ 10
It seems like your single cell RNAseq data does not already contain the Cell Barcodes or Unique Molecular Identifiers in the standard way -…
Comment: Demultiplexing bam file
by
GenoMax
129k
> Part of the header of the bam file So perhaps there are more samples. https://www.biostars.org/u/21477/: `grep "SM*" header_of_bam`. Is…
Answer: extract all fasta sequence from db v5
by
GenoMax
129k
If you need the fasta sequence download from NCBI here (146 GB zip compressed file) : https://ftp.ncbi.nih.gov/blast/db/FASTA/nr.gz
Comment: ScRNA data
by
GenoMax
129k
Is this from a SRA dataset? If so it is possible that you can get the correct information in `DataAccess` tab. Provide the accession number…
Comment: extract all fasta sequence from db v5
by
Pierre Lindenbaum
154k
is version 4 compatible with blast v5 ? try to use version 4....
Comment: Pre-processing for Agilent microarray data?
by
solarchan7
• 0
thank you!
Comment: Does the RNAseq data normal if the TPM value 3rd Qutile expression is near 10, b
by
alwayshope
▴ 20
Thanks a lot! Very helpful detailed guidance! Appreciate it a lot!
Answer: Does the RNAseq data normal if the TPM value 3rd Qutile expression is near 10, b
by
Dr William Klubinski
▴ 10
The values you are getting, with a third quartile of appx 10 and a max of appx 20,000, seem quite standard for RNA-Seq analysis. The RNA-se…
Comment: Demultiplexing bam file
by
Pierre Lindenbaum
154k
you don't talk about the size in your question
Comment: Demultiplexing bam file
by
hasani.iut6
▴ 60
so why the size of bam file is 40 gig?
Comment: Demultiplexing bam file
by
Pierre Lindenbaum
154k
> I want to separate every sample I don't understand. In your header there is only one sample : "`13.02.1402_POOL2"`
Comment: Error while running Megahit
by
Mensur Dlakic
★ 23k
We can't even begin to guess what the problem was without an error message.
Comment: DEgs RNAseq
by
dsull
★ 4.2k
Is this single-cell RNAseq or non-single-cell RNAseq? For single-cell, you typically don't do standard "differential gene expression analy…
Comment: Counting intronic reads in bulk RNA-seq
by
dsull
★ 4.2k
Correct, and I agree -- reads lying fully within introns are usually not counted for either single-cell or bulk. Inclusion of introns in a…
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