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1,038 results • Page
1 of 21
Sort: Rank
Rank
Views
Votes
Replies
1
vote
2
replies
117
views
Design matrix Differential expression analysis
RNA-seq
Differential-expression
30 minutes ago by
SHN
▴ 40
2
votes
3
replies
667
views
Issues with Mixture file when using CIBERSORTx
Deconvolution
CIBERSORTx
updated 1 hour ago by
vjanve
• 0 • written 7 months ago by
mateomejias
• 0
0
votes
0
replies
26
views
Association study using SNP data
Association
Allele
Parentage
SNP
2 hours ago by
drajangirija
• 0
0
votes
0
replies
26
views
GRCh38.gmap file
gnomix
gmap
3 hours ago by
lorena9132
• 0
0
votes
2
replies
76
views
creating batch colum for batch correction
batch
correction
combat
3 hours ago by
Expert
▴ 10
0
votes
4
replies
155
views
Segmentation error while using a tool
smalt
updated 5 hours ago by
Mensur Dlakic
★ 27k • written 12 hours ago by
Ruqaiya
• 0
0
votes
0
replies
33
views
Help with DGEList function
bioinformatics
6 hours ago by
Natali
• 0
0
votes
0
replies
38
views
Homer motif analysis
Homer
6 hours ago by
daffodil
▴ 10
0
votes
1
reply
80
views
HCL database download
database
HCL
human
updated 13 hours ago by
GenoMax
142k • written 13 hours ago by
sooni
▴ 20
1
vote
1
reply
980
views
News:
The GDC Legacy Archive is retiring soon.
genomic-data-commons
tcga
gdc
updated 15 hours ago by
lcordeiro
▴ 40 • written 14 months ago by
Zhenyu Zhang
★ 1.2k
0
votes
1
reply
194
views
Force PLINK2 to neglect chrX as the sex chromosome
PLINK2
updated 16 hours ago by
chrchang523
10k • written 4 days ago by
8armed
• 0
0
votes
5
replies
245
views
Easy way to find out which allele is minor allele from bed file?
plink
updated 16 hours ago by
chrchang523
10k • written 1 day ago by
curious
▴ 750
0
votes
0
replies
71
views
Quetion regarding WGCNA
WGCNA
Network-construction
updated 10 hours ago by
Ram
43k • written 18 hours ago by
deepak180001
• 0
0
votes
1
reply
115
views
visualize GSEA
enrichment
barplot
RNA-seq
GSEA
positive
updated 19 hours ago by
bk11
★ 2.4k • written 20 hours ago by
Rob
▴ 170
0
votes
1
reply
105
views
fastq screen aligner no specified.
BWA
Bowtie2
FastqScreen
updated 13 hours ago by
GenoMax
142k • written 20 hours ago by
Ximena
• 0
0
votes
1
reply
99
views
filtering before dada2
bbduk
qiime2
dada2
metagenomic
updated 10 hours ago by
Ram
43k • written 20 hours ago by
Valentina
• 0
0
votes
6
replies
307
views
Differential Expression Analysis using DESeq2 in R
deseq2
R
updated 20 hours ago by
swbarnes2
14k • written 1 day ago by
Erina
• 0
0
votes
1
reply
108
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 21 hours ago by
swbarnes2
14k • written 21 hours ago by
kalavattam
▴ 190
0
votes
1
reply
102
views
TaxID mapping file
annotation
blobtools
RNAseq
decontamination
transcriptomes
updated 22 hours ago by
GenoMax
142k • written 22 hours ago by
Lada
▴ 30
0
votes
0
replies
78
views
.lgen file has 3+ different alleles
PLINK
lgen
ped
1 day ago by
Emilie
• 0
0
votes
0
replies
76
views
vcf procesing for ML antigen prediction
formats
vcf
fastaq
HLA_imputation
HLA_typing
1 day ago by
Javier
• 0
0
votes
1
reply
104
views
Extracting mutation status from MAF files - TCGA
TCGA
maf
mutation
updated 10 hours ago by
Thanujay S
• 0 • written 1 day ago by
yahn
• 0
0
votes
0
replies
73
views
IGV interpretation for ATM gene for chromosome 11 for a deceased partient suspected of having melanoma
genetic
Variant
predisposition
1 day ago by
mikemakaveli1
• 0
0
votes
0
replies
74
views
Tissue-specific DEG analysis with DEseq2
DEseq2
RNA-seq
DEG
R
updated 1 day ago by
Ram
43k • written 1 day ago by
M.
▴ 30
0
votes
2
replies
134
views
Raw counts using stringtie
stringtie
RNA-seq
updated 1 day ago by
GenoMax
142k • written 1 day ago by
ahmad.sajad4541
• 0
0
votes
0
replies
69
views
Modify plot R mtDNA indel
plot
mtDNA
R
1 day ago by
marco.barr
▴ 90
0
votes
0
replies
133
views
Re-Import modified clusterProfiler's GSEA result from .csv for graphical output-generation (i.e. cnetplot, heatplot)
enrichplot
graphical_output
GSEA
clusterProfiler
1 day ago by
NorbertK
• 0
2
votes
2
replies
155
views
Analysis of intronic reads included scRNA-seq data
cell
single
updated 1 day ago by
t.montserrat.ayuso
▴ 10 • written 1 day ago by
carolofharvest
▴ 30
9
votes
9
replies
483
views
High Malat-1 expression in single cell data
cell
analysis
single
updated 1 day ago by
dsull
★ 6.0k • written 5 days ago by
carolofharvest
▴ 30
0
votes
2
replies
158
views
Downloading older version of a tool
Alignment
tools
12 hours ago by
Ruqaiya
• 0
0
votes
0
replies
86
views
Generating illumina interops SAV like plots for multiqc reports on HPC
visualization
illumina
ngs
sequencing
1 day ago by
rustykb
▴ 20
1
vote
1
reply
114
views
DSEQ2 analysis
DSEQ2
logfoldchane
updated 1 day ago by
ATpoint
82k • written 1 day ago by
adi.gershon1
• 0
3
votes
5
replies
206
views
Generating mpileup file using samtools
mpileup
samtools
updated 1 day ago by
Joe
21k • written 1 day ago by
Ruqaiya
• 0
0
votes
5
replies
267
views
6 follow
What purposes can TPM values be used for?
RNA-seq
TPM
Normalization
DESeq2
updated 1 day ago by
b.contreras.moreira
▴ 180 • written 2 days ago by
JH
• 0
1
vote
3
replies
221
views
Does comparing two different groups to a common third group introduce bias in the analysis?
DESEQ
RNAseq
updated 1 day ago by
ATpoint
82k • written 1 day ago by
Qi
• 0
0
votes
0
replies
86
views
News:
Cellosaurus release 49 is available
cell
biocuration
line
database
news
knowledgebase
1 day ago by
Amos Bairoch
▴ 120
2
votes
3
replies
223
views
Help with choosing a model species for Augustus for a de novo assembled genome.
augustus
annotation
assembly
genome
updated 1 day ago by
dthorbur
★ 1.9k • written 1 day ago by
Vijith
▴ 30
0
votes
0
replies
103
views
SIngle cell analysis
Seurat
scRNA-seq
Harmony
DoubletFinder
Merge
1 day ago by
Jeyong
• 0
0
votes
2
replies
688
views
homer not configured properly
Homer
makeTagDirectory
updated 1 day ago by
clairechung112
• 0 • written 23 months ago by
amahdi779
• 0
1
vote
3
replies
207
views
Bedtools merge minimum overlap?
bedtools
genomics
updated 1 day ago by
Alex Reynolds
35k • written 1 day ago by
SJP
• 0
0
votes
0
replies
98
views
Empty table plot using plotGseaTable()
FGSEA
19 hours ago by
Chris
▴ 260
0
votes
1
reply
146
views
VG : No reference-sense paths available in the graph; falling back to generic paths.
vg
updated 1 day ago by
anovak
▴ 120 • written 2 days ago by
Hang
• 0
1
vote
3
replies
194
views
DiffBind: no peaks in DBA
MACS2
DiffBind
ChIP-seq
updated 1 day ago by
jared.andrews07
★ 16k • written 2 days ago by
yvonneh
▴ 10
3
votes
5
replies
261
views
Converting CRAM to FastQ
GATK
samtools
cram
SamToFastq
fastq
22 hours ago by
Maverick
▴ 10
3
votes
8
replies
6.5k
views
7 follow
GATK genomicsDBimport intervals for WGS
gatk
genomicsdbimport
updated 1 day ago by
Sd
• 0 • written 5.1 years ago by
Nicolas Rosewick
11k
0
votes
2
replies
158
views
Base Quality Score Recalibration with different reference genome
SNPs
GATK
BQSR
RNA-seq
1 day ago by
dtnondorf
• 0
0
votes
1
reply
185
views
Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA2 - where to go from here?
nf-core
16S
amplicon
dada2
ampliseq
updated 1 day ago by
Chris Dean
▴ 390 • written 1 day ago by
sovrappensiero
▴ 90
1
vote
2
replies
208
views
RNA-seq data for deep learning classification
rna-seq
1 day ago by
yahn
• 0
2
votes
6
replies
314
views
How to access TCGA samples that were treated with a specific drug?
TCGA
RNA-seq
1 day ago by
Qroid
▴ 40
0
votes
1
reply
502
views
Loss of 'var' using concatenation of AnnData objects
Scanpy
AnnData
updated 2 days ago by
Hugo
• 0 • written 4 months ago by
Rachel
• 0
1,038 results • Page
1 of 21
Recent Votes
Answer: Design matrix Differential expression analysis
A: extract dendrogram cluster from pheatmap
extract dendrogram cluster from pheatmap
Answer: Searching for gene in multiple genomes
Comment: RNA velocity for smart-seq2 dataset
Answer: RNA velocity for smart-seq2 dataset
Answer: RNA velocity for smart-seq2 dataset
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Recent Awards •
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Commentator
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dsull
★ 6.0k
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★ 1.7k
Popular Question
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drajangirija
• 0
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Thanujay S
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SHN
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Rob
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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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