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24 results • Page
1 of 1
Sort: Rank
Rank
Views
Votes
Replies
1
vote
2
replies
128
views
Design matrix Differential expression analysis
RNA-seq
Differential-expression
2 hours ago by
SHN
▴ 40
2
votes
3
replies
678
views
Issues with Mixture file when using CIBERSORTx
Deconvolution
CIBERSORTx
updated 2 hours ago by
vjanve
• 0 • written 7 months ago by
mateomejias
• 0
0
votes
0
replies
37
views
Association study using SNP data
Association
Allele
Parentage
SNP
4 hours ago by
drajangirija
• 0
0
votes
0
replies
36
views
GRCh38.gmap file
gnomix
gmap
4 hours ago by
lorena9132
• 0
0
votes
2
replies
86
views
creating batch colum for batch correction
batch
correction
combat
4 hours ago by
Expert
▴ 10
0
votes
4
replies
162
views
Segmentation error while using a tool
smalt
updated 6 hours ago by
Mensur Dlakic
★ 27k • written 14 hours ago by
Ruqaiya
• 0
0
votes
0
replies
39
views
Help with DGEList function
bioinformatics
7 hours ago by
Natali
• 0
0
votes
0
replies
44
views
Homer motif analysis
Homer
8 hours ago by
daffodil
▴ 10
0
votes
1
reply
82
views
HCL database download
database
HCL
human
updated 14 hours ago by
GenoMax
142k • written 15 hours ago by
sooni
▴ 20
1
vote
1
reply
986
views
News:
The GDC Legacy Archive is retiring soon.
genomic-data-commons
tcga
gdc
updated 17 hours ago by
lcordeiro
▴ 40 • written 14 months ago by
Zhenyu Zhang
★ 1.2k
0
votes
1
reply
196
views
Force PLINK2 to neglect chrX as the sex chromosome
PLINK2
updated 17 hours ago by
chrchang523
10k • written 4 days ago by
8armed
• 0
0
votes
5
replies
248
views
Easy way to find out which allele is minor allele from bed file?
plink
updated 17 hours ago by
chrchang523
10k • written 1 day ago by
curious
▴ 750
0
votes
0
replies
73
views
Quetion regarding WGCNA
WGCNA
Network-construction
updated 12 hours ago by
Ram
43k • written 20 hours ago by
deepak180001
• 0
0
votes
1
reply
117
views
visualize GSEA
enrichment
barplot
RNA-seq
GSEA
positive
updated 20 hours ago by
bk11
★ 2.4k • written 22 hours ago by
Rob
▴ 170
0
votes
1
reply
108
views
fastq screen aligner no specified.
BWA
Bowtie2
FastqScreen
updated 14 hours ago by
GenoMax
142k • written 22 hours ago by
Ximena
• 0
0
votes
1
reply
102
views
filtering before dada2
bbduk
qiime2
dada2
metagenomic
updated 12 hours ago by
Ram
43k • written 22 hours ago by
Valentina
• 0
0
votes
6
replies
309
views
Differential Expression Analysis using DESeq2 in R
deseq2
R
updated 21 hours ago by
swbarnes2
14k • written 1 day ago by
Erina
• 0
0
votes
1
reply
110
views
Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read reverse strand" (flag 32/0x20)
PE
BAM
SAM
flag
paired-end
updated 22 hours ago by
swbarnes2
14k • written 22 hours ago by
kalavattam
▴ 190
0
votes
1
reply
111
views
Extracting mutation status from MAF files - TCGA
TCGA
maf
mutation
updated 11 hours ago by
Thanujay S
• 0 • written 1 day ago by
yahn
• 0
0
votes
2
replies
160
views
Downloading older version of a tool
Alignment
tools
14 hours ago by
Ruqaiya
• 0
0
votes
0
replies
100
views
Empty table plot using plotGseaTable()
FGSEA
21 hours ago by
Chris
▴ 260
5
votes
5
replies
560
views
Tutorial:
how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix
RNAseq
R
updated 22 hours ago by
Mbofire
• 0 • written 9 days ago by
Ming Tommy Tang
★ 3.9k
4
votes
15
replies
1.6k
views
how to test for differential expression in samples where a global increase in gene expression is expected
edgeR
DESeq
Differential-Expression
RNA-Seq
updated 14 hours ago by
Gordon Smyth
★ 7.1k • written 4 months ago by
raplayer
▴ 10
2
votes
2
replies
2.6k
views
Pindel Segmentation Fault Error
pindel
updated 6 hours ago by
Ruqaiya
• 0 • written 10.2 years ago by
Yuelin
▴ 20
24 results • Page
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Recent Votes
Answer: Design matrix Differential expression analysis
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Answer: RNA velocity for smart-seq2 dataset
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Recent Awards •
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Commentator
to
dsull
★ 6.0k
Scholar
to
BioinfGuru
★ 1.7k
Popular Question
to
drajangirija
• 0
Popular Question
to
Thanujay S
• 0
Popular Question
to
SHN
▴ 40
Popular Question
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Rob
▴ 170
Scholar
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GenoMax
142k
Recent Replies
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 …
Comment: Extracting mutation status from MAF files - TCGA
by
Thanujay S
• 0
Hey! Can you explain the question further? What have you tried?
Comment: Downloading older version of a tool
by
Ruqaiya
• 0
I tried the 2nd option only. I got the files of older version from the author but that version isn't working on my WSL, it's showing Segmen…
Comment: filtering before dada2
by
GenoMax
142k
> I encountered a significant decrease in the percentage of merged reads. You can check with `bbmerge.sh` from BBMap suite to see how many…
Comment: HCL database download
by
GenoMax
142k
Isn't the download link available above the plot: http://bis.zju.edu.cn/HCL/data/DGE/Adult-Transverse-Colon1_dge.txt.gz
Comment: fastq screen aligner no specified.
by
GenoMax
142k
You need to change this configuration file to point it to the location where the aligner executable can be found. So as an example followi…
Answer: Design matrix Differential expression analysis
by
Gordon Smyth
★ 7.1k
The expression levels do not change but the way that you have parametrized the expression levels does change. The two design matrices give…
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