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19 results • Page
1 of 1
Sort: Views
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Views
Votes
Replies
2
votes
2
replies
2.6k
views
Pindel Segmentation Fault Error
pindel
updated 22 hours ago by
Ruqaiya
• 0 • written 10.2 years ago by
Yuelin
▴ 20
3
votes
0
replies
1.1k
views
Tool:
Sars-Cov-2 Genome & ACE 2 Exploration
sequence
alignment
SNP
genome
10 minutes ago by
Ibrahim Tanyalcin
★ 1.2k
1
vote
2
replies
1.0k
views
News:
The GDC Legacy Archive is retiring soon.
genomic-data-commons
tcga
gdc
2 hours ago by
Zhenyu Zhang
★ 1.2k
2
votes
3
replies
736
views
Issues with Mixture file when using CIBERSORTx
Deconvolution
CIBERSORTx
updated 18 hours ago by
vjanve
• 0 • written 7 months ago by
mateomejias
• 0
9
votes
9
replies
512
views
High Malat-1 expression in single cell data
single-cell
updated 15 hours ago by
Ram
43k • written 5 days ago by
carolofharvest
▴ 30
2
votes
7
replies
358
views
How to access TCGA samples that were treated with a specific drug?
TCGA
RNA-seq
updated 2 hours ago by
Zhenyu Zhang
★ 1.2k • written 2 days ago by
Qroid
▴ 40
2
votes
3
replies
255
views
Design matrix Differential expression analysis
RNA-seq
Differential-expression
updated 8 hours ago by
Gordon Smyth
★ 7.1k • written 1 day ago by
SHN
▴ 40
0
votes
4
replies
242
views
Segmentation error while using a tool
smalt
updated 22 hours ago by
Mensur Dlakic
★ 27k • written 1 day ago by
Ruqaiya
• 0
2
votes
2
replies
178
views
Analysis of intronic reads included scRNA-seq data
single-cell
updated 15 hours ago by
Ram
43k • written 2 days ago by
carolofharvest
▴ 30
0
votes
2
replies
157
views
creating batch colum for batch correction
batch-correction
combat
updated 15 hours ago by
Ram
43k • written 22 hours ago by
Expert
▴ 10
4
votes
2
replies
144
views
GRCh38.gmap file
gnomix
gmap
11 hours ago by
lorena9132
▴ 10
0
votes
1
reply
143
views
visualize GSEA
barplot
RNA-seq
GSEA
enrichment
updated 15 hours ago by
Ram
43k • written 1 day ago by
Rob
▴ 170
1
vote
1
reply
137
views
DSEQ2 analysis
DESEQ2
logfoldchange
updated 15 hours ago by
Ram
43k • written 2 days ago by
adi.gershon1
• 0
0
votes
1
reply
128
views
Association study using SNP data
Association
Allele
Parentage
SNP
updated 12 hours ago by
Mathew
▴ 30 • written 20 hours ago by
drajangirija
• 0
0
votes
0
replies
72
views
Help with DGEList function
DGEList
R
updated 15 hours ago by
Ram
43k • written 23 hours ago by
Natali
• 0
0
votes
0
replies
71
views
LD-prune variants while maintaining a list of SNPs
snp
vcf
filtering
independent
linkage
13 hours ago by
Jautis
▴ 530
0
votes
0
replies
53
views
Forum:
Seeking Bioinformatics/Drug Design Opportunities - PhD in Pharmacology with Experience in RNA-seq, CADD & Deep Learning Molecular Generation
search
job
5 hours ago by
tulip
• 0
0
votes
0
replies
31
views
Problem with Seurat package in PercentageFeatureSet function
cell
single
3 hours ago by
Yoosef
▴ 60
0
votes
0
replies
7
views
Seurat V5 integration
Seurat
samples
integration
combine
2 minutes ago by
starswillfade
▴ 10
19 results • Page
1 of 1
Recent Votes
Comment: Raw counts using stringtie
Comment: Raw counts using stringtie
Answer: GRCh38.gmap file
Comment: GRCh38.gmap file
Answer: GRCh38.gmap file
Answer: GRCh38.gmap file
Answer: Design matrix Differential expression analysis
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Recent Replies
Comment: The GDC Legacy Archive is retiring soon.
by
Zhenyu Zhang
★ 1.2k
If you are talking about methylation idat files, they were all migrated from legacy to the data portal. If you are talking about other pl…
Comment: How to access TCGA samples that were treated with a specific drug?
by
Zhenyu Zhang
★ 1.2k
These TCGA samples were taken 10 ~ 20 years ago, and there is no way they have been treated by the modern immunotherapy. Are you sure tha…
Comment: Design matrix Differential expression analysis
by
Gordon Smyth
★ 7.1k
> When is it recommended to use the design <- cbind(Intercept=1,Group=c(-1,-1,-1,1,1,1)) It is not recommended. No such code appears anywh…
Comment: GRCh38.gmap file
by
lorena9132
▴ 10
Hi Mathew, The .txt files provided in the link differ from the .gmap files, but after several attempts, I succeeded in generating the .gma…
Answer: GRCh38.gmap file
by
Mathew
▴ 30
Hi, I have spent some time searching for a GRCH38 map file for you. I have found a certain publication that uses a hg38 genetic map file…
Answer: Association study using SNP data
by
Mathew
▴ 30
Hi, You asked three questions so I will attempt to help the best I can **What should be the optimal GC score cutoff** It sounds li…
Comment: Design matrix Differential expression analysis
by
SHN
▴ 40
Thank you for your explanation. I am working on the cell lines and I am investigating the effect of the treatment on the expression level, …
Answer: Issues with Mixture file when using CIBERSORTx
by
vjanve
• 0
I ran into same issue of "duplicated gene symbol(s)": 1: In CIBERSORTxFractions(sigmatrix = sigmatrix, mixture = mixture, : 22292 dup…
Comment: creating batch colum for batch correction
by
Expert
▴ 10
Thank you for your response. These samples were collected from the same patient at different time points(day 0, 8 and 18) and these are ind…
Comment: creating batch colum for batch correction
by
ATpoint
82k
Not sure I follow. Can you first of all describe which comparisons you want to make, pretending there was no batch effect at all. Write dow…
Comment: Pindel Segmentation Fault Error
by
Ruqaiya
• 0
This the tool still problematic?
Comment: Segmentation error while using a tool
by
Ruqaiya
• 0
Thank you for the advice, i'll keep that in mind.
Comment: Segmentation error while using a tool
by
Ruqaiya
• 0
I am trying to reproduce some bioinformatics data from a research paper-[this paper][1] as i was asked to work on an MRSA bioinfo project, …
Answer: Segmentation error while using a tool
by
Mensur Dlakic
★ 27k
Most likely you didn't do anything wrong. Going by your previous post that you have only 8 GB of RAM, the most likely reason is the lack of…
Comment: Segmentation error while using a tool
by
Thanujay S
• 0
Hey @Ruqaiya! Can you please give more details on why smalt is opted here? According to what I can see, the tool has become obsolete! Why …
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