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116,756 results • Page
1 of 2336
Sort: Rank
Rank
Views
Votes
Replies
1
vote
2
replies
129
views
Design matrix Differential expression analysis
RNA-seq
Differential-expression
2 hours ago by
SHN
▴ 40
2
votes
3
replies
679
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
38
views
Association study using SNP data
Association
Allele
Parentage
SNP
4 hours ago by
drajangirija
• 0
795
votes
167
replies
142k
views
109 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 3 months ago by
Biostar
2.7k • written 7.4 years ago by
Istvan Albert
100k
0
votes
0
replies
37
views
GRCh38.gmap file
gnomix
gmap
5 hours ago by
lorena9132
• 0
0
votes
2
replies
86
views
creating batch colum for batch correction
batch
correction
combat
5 hours ago by
Expert
▴ 10
0
votes
4
replies
163
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
40
views
Help with DGEList function
bioinformatics
8 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 15 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 18 hours ago by
chrchang523
10k • written 4 days ago by
8armed
• 0
0
votes
5
replies
249
views
Easy way to find out which allele is minor allele from bed file?
plink
updated 18 hours ago by
chrchang523
10k • written 1 day ago by
curious
▴ 750
0
votes
0
replies
74
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
109
views
fastq screen aligner no specified.
BWA
Bowtie2
FastqScreen
updated 15 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 23 hours ago by
swbarnes2
14k • written 23 hours ago by
kalavattam
▴ 190
0
votes
1
reply
105
views
TaxID mapping file
annotation
blobtools
RNAseq
decontamination
transcriptomes
updated 1 day ago by
GenoMax
142k • written 1 day ago by
Lada
▴ 30
0
votes
0
replies
80
views
.lgen file has 3+ different alleles
PLINK
lgen
ped
1 day ago by
Emilie
• 0
0
votes
0
replies
78
views
vcf procesing for ML antigen prediction
formats
vcf
fastaq
HLA_imputation
HLA_typing
1 day ago by
Javier
• 0
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
0
replies
75
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
76
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
136
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
71
views
Modify plot R mtDNA indel
plot
mtDNA
R
1 day ago by
marco.barr
▴ 90
0
votes
0
replies
142
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
157
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
485
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
160
views
Downloading older version of a tool
Alignment
tools
14 hours ago by
Ruqaiya
• 0
0
votes
0
replies
88
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
116
views
DSEQ2 analysis
DSEQ2
logfoldchane
updated 1 day ago by
ATpoint
82k • written 1 day ago by
adi.gershon1
• 0
3
votes
5
replies
208
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
270
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
224
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
89
views
News:
Cellosaurus release 49 is available
cell
biocuration
line
database
news
knowledgebase
1 day ago by
Amos Bairoch
▴ 120
2
votes
3
replies
225
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
105
views
SIngle cell analysis
Seurat
scRNA-seq
Harmony
DoubletFinder
Merge
1 day ago by
Jeyong
• 0
0
votes
2
replies
690
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
209
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
100
views
Empty table plot using plotGseaTable()
FGSEA
21 hours ago by
Chris
▴ 260
0
votes
1
reply
148
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
197
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
263
views
Converting CRAM to FastQ
GATK
samtools
cram
SamToFastq
fastq
1 day 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
160
views
Base Quality Score Recalibration with different reference genome
SNPs
GATK
BQSR
RNA-seq
1 day ago by
dtnondorf
• 0
0
votes
1
reply
187
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 2 days ago by
sovrappensiero
▴ 90
1
vote
2
replies
210
views
RNA-seq data for deep learning classification
rna-seq
1 day ago by
yahn
• 0
2
votes
6
replies
317
views
How to access TCGA samples that were treated with a specific drug?
TCGA
RNA-seq
1 day ago by
Qroid
▴ 40
116,756 results • Page
1 of 2336
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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dsull
★ 6.0k
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★ 1.7k
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drajangirija
• 0
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• 0
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SHN
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Rob
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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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