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14 results • Page
1 of 1
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Votes
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0
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3
views
how to add TCGA CNV as covariate for matrixeqtl
covariate
matrixeqtl
CNV
12 minutes ago by
Binghong
▴ 20
0
votes
0
replies
10
views
Process mining in bioinformatics
processmining
21 minutes ago by
Cygi
• 0
0
votes
0
replies
9
views
Getting an "double free or corruption (out)" error when running wigToBigWig
wigToBigwig
41 minutes ago by
rls_08
▴ 40
0
votes
0
replies
7
views
Get Count matrix of geodatasets
geo
R
1 hour ago by
anasjamshed
▴ 120
0
votes
0
replies
9
views
Differences between GSVA and GSEA?
gsea
genome
genetics
gene
gsva
1 hour ago by
DS
▴ 20
0
votes
0
replies
22
views
Recommendations on Public Linux server for academics purposes
server
linux
rna-seq
2 hours ago by
Ant
• 0
0
votes
0
replies
63
views
Any straightforward way to re-bin a bigWig file?
bigwig
9 hours ago by
rls_08
▴ 40
0
votes
0
replies
101
views
How to get BEAGLE files from VCF with angsd?
angsd
vcf
populationgenetics
beagle
pcangsd
16 hours ago by
Begonia_pavonina
▴ 90
0
votes
0
replies
128
views
How to find p-values for annotated methylated regions using methylkit and genomation
NGS
bioinformatics
pvalue
annotation
methylationarray
17 hours ago by
Saransh
• 0
0
votes
1
reply
230
views
TCGA-BRCA tissue and RNAseq problem
NIH
RNAseq
GDC
TCGA-BRCA
updated 18 hours ago by
pinheirofabiano
▴ 10 • written 1 day ago by
reventropy2003
• 0
0
votes
2
replies
211
views
Gene family classification using RNA-seq data
RNA_seq
gene_expression
gene_family
16 hours ago by
Dion
• 0
0
votes
2
replies
220
views
Quality control of Chip-seq data (NRF and PCB)
control
library
quality
PCB
Chip-seq
NRF
14 hours ago by
michelafrancesconi9
• 0
0
votes
0
replies
106
views
Nucleotide substitution model and neighbor-joining tree
phylogeny
substitution
mega
neighbor-joining
modeltest
14 hours ago by
poecile.pal
▴ 50
1
vote
4
replies
443
views
SKAT in R
pvalue
skat
snp
18 hours ago by
Eliza
▴ 20
14 results • Page
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Recent Votes
Answer: how can i filter a sam file from a paf file
Answer: Align miRNA library (small RNA-seq) without trimming
Answer: Snakemake workflow for trimmomatic
C: Adjust for covariates
Comment: syntax errors when running part3 all-against-all
Picard LiftOver rejecting all Variants
Comment: pyCirclize - Circular visualization in Python
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anasjamshed
▴ 120
Teacher
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Papyrus
★ 2.4k
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Recent Replies
Comment: Diffbind dba.count doesn't give FRiP score
by
gyspace
• 0
I found your email in https://bioinfotraining.bio.cam.ac.uk/staff/rory-stark-phd, is the email right? I sent a google drive link to you. If…
Comment: how can i filter a sam file from a paf file
by
colindaven
4.6k
Just save yourself a lot of pain and learn to filter the sam/bam file efficiently. It is much more of a widespread standard than PAF.
Comment: Snakemake workflow for trimmomatic
by
GenoMax
127k
Please accept this answer (green check mark) to provide closure to this thread.
Comment: syntax errors when running part3 all-against-all
by
Sofia
• 0
When I started with the gz all-vs-all files for CHICK and ANOCA and started oma, everything ran fine, I got output. Then, in the same direc…
Comment: Quality control of Chip-seq data (NRF and PCB)
by
michelafrancesconi9
• 0
Can you explain me better? Because for the NRF I do : a) samtools view -c .bam b)samtools view -c -F 260 .bam then b/a and as a bam fi…
Comment: pyCirclize - Circular visualization in Python
by
karenkvn
▴ 40
Thank you for responding so quickly - this works perfectly!
Comment: pyCirclize - Circular visualization in Python
by
moshi
▴ 110
Please install Biopython with v1.80 or higher. If biopython>=1.80, there should be no errors.
Comment: Gene family classification using RNA-seq data
by
Dion
• 0
well, I have been given the task to retrieve gene family/categorization. I found sveral papers on family classification, but no actual pack…
Comment: pyCirclize - Circular visualization in Python
by
karenkvn
▴ 40
Thank you for this wonderful programme! I am plotting a bacterial chromosome and find that when I plot the NC_000913 chromosome using the e…
Comment: SKAT in R
by
Eliza
▴ 20
@acvill can you sujjest maybe pther tools , methods for this ? ( also for every SNP i have data how many patients had the hetro/homozygous…
Comment: TCGA-BRCA tissue and RNAseq problem
by
pinheirofabiano
▴ 10
Go to https://portal.gdc.cancer.gov > Exploration > select TCGA and the cancer type you want > select case ID to download the files and hav…
Comment: Snakemake workflow for trimmomatic
by
antoine.fauchois92
• 0
Thank you very much for your reply ! It's working now !
Comment: Dependent p values
by
Eliza
▴ 20
@lchart I'm sorry for asking another of questions but I'm new to this field , can you please explain a little more how to use SKAT , saige…
Comment: How to deal with the probe id mapping to multiple gene ids?
by
dare_devil
★ 1.7k
similar question [here][1], [here][2] and [here][3] [1]: https://support.bioconductor.org/p/54838/ [2]: https://support.bioconductor.…
Comment: How to deal with the probe id mapping to multiple gene ids?
by
dare_devil
★ 1.7k
@genomax I have used the same platform file only. If you look at probe id and their corresponding `Gene Symbol` or `ENTREZ_GENE_ID` you can…
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