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21 results • Page
1 of 1
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
8
views
lncRNA
tcga
lncrna
28 minutes ago by
jain72744
▴ 10
0
votes
0
replies
15
views
Mouse ribosome sequences in fasta format
fasta
mm10
rRNA
2 hours ago by
octpus616
▴ 100
0
votes
0
replies
29
views
BWA alignment
Samtools
bam
3 hours ago by
Vahid
• 0
0
votes
1
reply
166
views
Nomalization - TCGA, RNA-seq and Microarray
TCGA
RNA-seq
Nomalization
Microarray
updated 6 hours ago by
Zhenyu Zhang
★ 1.2k • written 3 days ago by
jain72744
▴ 10
1
vote
5
replies
454
views
Tissue-specific DEG analysis with DEseq2
DEseq2
RNA-seq
DEG
R
updated 11 hours ago by
arctic
▴ 40 • written 9 days ago by
M.
▴ 30
0
votes
0
replies
55
views
Manual Assembly and Protein Translation, HELP, assignment revision
sequence
university
assembly
protein
genomics
12 hours ago by
rackbersingh
• 0
1
vote
1
reply
180
views
How to remove multiple batch effects from RNA-seq data before limma differential gene expression analysis?
batch
ComBat-seq
limma
RNA-seq
removeBatchEffect
updated 8 hours ago by
ATpoint
82k • written 13 hours ago by
t.fortunato.asquini
• 0
0
votes
1
reply
169
views
Practical Haplotype Graph v2 not finding correct paths
Pangenome
PHG
graph
updated 14 hours ago by
pjb39
▴ 200 • written 2 days ago by
beantkapoor16
• 0
0
votes
2
replies
145
views
Output file of satools flagstat empty
samtools-flagstat
updated 14 hours ago by
Mathew
▴ 100 • written 16 hours ago by
ramendra.sarma
• 0
0
votes
0
replies
58
views
How can I create a eigencorplot of pca created from deseq2 object with PCAtools
eigencorplot
PCAtools
deseq2
pca
15 hours ago by
BioinfGuru
★ 1.7k
2
votes
8
replies
267
views
joint callset and vcf sorting, unknown TAG issue
sort
bcftools
GLNexus
merge
VCF
updated 15 hours ago by
Pierre Lindenbaum
161k • written 18 hours ago by
Matteo Ungaro
▴ 100
0
votes
0
replies
77
views
News:
Online course: An Introduction to Nanopore Direct RNA Sequencing
Nanopore
RNAseq
22 hours ago by
carlopecoraro2
★ 2.5k
6
votes
7
replies
287
views
Longest transcript variant per gene
transcript
longest
variant
orthofinder
10 hours ago by
sansan_96
▴ 90
0
votes
3
replies
271
views
Adata.raw.X in LIANA, something wrong with conversion from Seurat to adata in python.
k
updated 6 hours ago by
fracarb8
★ 1.6k • written 1 day ago by
beginner123
• 0
0
votes
6
replies
329
views
Is it Possible to "Merge" data from Replicates within a VCF SNP File
snp
vcf
plink
bioinformatics
genomics
updated 12 hours ago by
Pierre Lindenbaum
161k • written 2 days ago by
ajbarrett98
• 0
0
votes
11
replies
428
views
In IGV is this a heterogeneous mutation or false call?
mutations
IGV
heterogeneous
10 hours ago by
Tuck898
• 0
0
votes
5
replies
254
views
How to convert normalized BigWig file to count matrix?
count-matrix
BigWig
2 hours ago by
feather-W
• 0
0
votes
2
replies
199
views
Obtaining Infinium Methylation450K manifest for hg38
TCGA
hg38
methylation
Illumina
updated 6 hours ago by
Zhenyu Zhang
★ 1.2k • written 4 days ago by
elisheva
▴ 120
3
votes
6
replies
443
views
install package: package ‘gmwm’ is not available for this version of R
r
updated 5 hours ago by
Pine
▴ 20 • written 7 days ago by
snajafy
• 0
0
votes
2
replies
269
views
Extracting mutation status from MAF files - TCGA
TCGA
maf
mutation
updated 6 hours ago by
Zhenyu Zhang
★ 1.2k • written 9 days ago by
yahn
• 0
6
votes
5
replies
2.3k
views
Tophat multiple or unique mapping criteria
RNA-Seq
updated 16 hours ago by
Ruqaiya
• 0 • written 6.7 years ago by
maple964
• 0
21 results • Page
1 of 1
Recent Votes
Comment: How to remove multiple batch effects from RNA-seq data before limma differential
Comment: automatic clustering annotation using python
automatic clustering annotation using python
Answer: How to compute TPM normalized values for TCGA miRNA data?
C: Convert .Txt File To Bed File
A: Get nonoverlapping regions of two bed files
Get nonoverlapping regions of two bed files
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Recent Awards •
All
Popular Question
to
rj.rezwan
• 0
Scholar
to
colindaven
6.4k
Scholar
to
pjb39
▴ 200
Popular Question
to
Jen
▴ 70
Scholar
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Pierre Lindenbaum
161k
Popular Question
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Michael
54k
Popular Question
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Kai_Qi
▴ 130
Recent Replies
Comment: How to convert normalized BigWig file to count matrix?
by
feather-W
• 0
Hi ATpoint, Thanks for your reply!
Comment: How to convert normalized BigWig file to count matrix?
by
feather-W
• 0
Hi Pierre, Thanks for your reply! I want to get a feature count matrix from coverage data stored in BigWig files. And this BigWig file ha…
Comment: Extracting mutation status from MAF files - TCGA
by
Zhenyu Zhang
★ 1.2k
you can assume all genes without mutation is WT (easy) while controlling for (difficult) - coverage - capture region - germline - the …
Comment: Obtaining Infinium Methylation450K manifest for hg38
by
Zhenyu Zhang
★ 1.2k
Since you are getting data from the GDC, analysis-related reference/annotations can be found in the GDC reference page here https://gdc.can…
Comment: Adata.raw.X in LIANA, something wrong with conversion from Seurat to adata in py
by
fracarb8
★ 1.6k
I saw that, but considering that your analysis is in seurat and that both liana and liana+ are from the same developers, it might be quicke…
Answer: Nomalization - TCGA, RNA-seq and Microarray
by
Zhenyu Zhang
★ 1.2k
You can rank normalize them, but to tell the truth, I won't trust any conclusion you can draw from such combined data. The recommended …
Comment: How to remove multiple batch effects from RNA-seq data before limma differential
by
ATpoint
82k
Include confounders into the limma design. No need for upfront removal. Note that libsize is taken care of by normalizing usually. Are you …
Comment: Longest transcript variant per gene
by
sansan_96
▴ 90
Thank you very much, success in your projects.
Comment: In IGV is this a heterogeneous mutation or false call?
by
Tuck898
• 0
Thanks for the input :)
Comment: install package: package ‘gmwm’ is not available for this version of R
by
Pine
▴ 20
This seems to indicate that the package itself (or packages it depends on) are not compatible with the R version you are using. Next step c…
Answer: Tissue-specific DEG analysis with DEseq2
by
arctic
▴ 40
Not my area of expertise but GTEx portal seems to offer visual comparison of expression across tissues, maybe checking their pipeline could…
Comment: Is it Possible to "Merge" data from Replicates within a VCF SNP File
by
Pierre Lindenbaum
161k
> I think I am mostly struggling with what would need to be coded to my dataset here and how to run this loop on my set in general. i do…
Comment: Is it Possible to "Merge" data from Replicates within a VCF SNP File
by
ajbarrett98
• 0
Pierre, I am a novice at all of this in general and I have never used Java-based programming before. I may not be able to properly wrangl…
Answer: Practical Haplotype Graph v2 not finding correct paths
by
pjb39
▴ 200
There have been a couple of bugs found that affect imputation accuracy, one in build-kmer-index and one in find-paths. The find-paths bug o…
Comment: Output file of satools flagstat empty
by
Mathew
▴ 100
Hi, In your samtools flagstat, -o specifies the output format. This can be set to 'default', 'json', or 'tsv'. If -o is not specified , t…
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