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119,305 results • Page
1 of 2387
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1
vote
11
replies
136
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Question about edgeR p-values/FDR values
edgeR
updated 21 minutes ago by
dariober
15k • written 11 hours ago by
Ronin
▴ 10
0
votes
1
reply
54
views
Plot query cells on top of reference cells in UMAP
R
Integration
Seurat
updated 56 minutes ago by
Bastien Hervé
5.7k • written 5 hours ago by
saicchan
• 0
0
votes
1
reply
173
views
Is it necessary to adjust genome to the same strand direction?
strand-direction
vg
updated 1 hour ago by
Xian
▴ 60 • written 5 days ago by
Yao
▴ 30
0
votes
0
replies
11
views
xCell output and immune cell ratio
statisitcs
data
immunedeconv
variations
1 hour ago by
a.stef.44
▴ 10
0
votes
1
reply
20
views
Spades Genome Assembly
genome
spades
assembly
updated 29 minutes ago by
dthorbur
★ 2.5k • written 1 hour ago by
Umer
▴ 120
0
votes
2
replies
61
views
Error in Trinity installation
Trinity
updated 2 hours ago by
Pierre Lindenbaum
164k • written 6 hours ago by
ongchip
• 0
1
vote
9
replies
3.6k
views
8 follow
Bam files not accepted in dba.count
samtools
diffbind
dba.count
bam
updated 9 hours ago by
katie_kat
• 0 • written 3.7 years ago by
corinne_hutfilz
• 0
0
votes
0
replies
56
views
How to normalize gene abundance from long read metagenomic data?
normalization
metagenomics
long-read
gene-abundance
10 hours ago by
Adrián
• 0
820
votes
169
replies
157k
views
110 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 5 weeks ago by
Biostar
3.0k • written 7.9 years ago by
Istvan Albert
101k
0
votes
0
replies
60
views
SILVA vs PR2 vs both for 18S metabarcoding?
taxonomy
18S
metabarcoding
11 hours ago by
hjarnek
▴ 20
0
votes
0
replies
75
views
Your suggestion how to annotate cell type from visium data
spatial-transcriptomics
11 hours ago by
Chris
▴ 340
0
votes
0
replies
55
views
HAPMIX : interpretation of the 16 probabilities generated when run in DIPLOID mode
hapmix
14 hours ago by
cshreya
• 0
0
votes
3
replies
151
views
Snakemake expand(): using a helper function (zip) and imputing wildcards?
snakemake
updated 1 hour ago by
Michael
55k • written 18 hours ago by
adixon3
• 0
0
votes
0
replies
59
views
Determing the effect of directionality on gene fusions
fusions
star-fusion
16 hours ago by
Ben
▴ 20
1
vote
5
replies
1.0k
views
failing to install rMATS
rMATS
updated 15 hours ago by
Jeremy Leipzig
22k • written 8 months ago by
thomas.heigl.ibk
• 0
1
vote
7
replies
224
views
Unable to view BAM files in IGV
macOS
igv
updated 20 hours ago by
Pierre Lindenbaum
164k • written 20 hours ago by
N-may
▴ 10
0
votes
0
replies
77
views
Seeking Guidance on WGBS Analysis for F1-Hybrid Mapping
Methylation
Bismark
WGBS
Mapping
Hybrid
21 hours ago by
binaryCode
▴ 10
7
votes
5
replies
224
views
Is there an elegant way to deal with the version indicator in reference FASTA file
FASTA
RefSeq
updated 10 hours ago by
shenwei356
8.6k • written 22 hours ago by
Xiaokang
▴ 80
0
votes
3
replies
141
views
VG giraffe autoindex and alignement mapping warning "Refusing to perform too-large rescue alignment"
variant
calling
pangenome
giraffe
vg
updated 1 hour ago by
Xian
▴ 60 • written 22 hours ago by
s_135
▴ 10
2
votes
2
replies
136
views
DeNovo Assembly - Assigning gene description
DeNovoAssembly
FunctionalAnnotation
Genedescription
WGS
updated 21 hours ago by
Michael
55k • written 1 day ago by
Sowmya Pulapet
▴ 70
2
votes
2
replies
113
views
statistical testing for MS/MS proteomics bulk samples
DEG
proteomics
updated 22 hours ago by
ATpoint
85k • written 1 day ago by
QX
▴ 60
1
vote
1
reply
118
views
What's going on with Ensembl?
biomaRt
ensembl
updated 21 hours ago by
GenoMax
146k • written 23 hours ago by
yura.grabovska
▴ 600
4
votes
16
replies
359
views
Gatk haplotyper
tumor
normal
haplotyper
Gatk
updated 49 minutes ago by
Michael
55k • written 1 day ago by
prs
▴ 20
2
votes
3
replies
323
views
Paired-end sequencing with inconsistent quality/number of reads
paired-end
NGS
STAR
flowcell
alignment
1 day ago by
anissa
• 0
0
votes
0
replies
70
views
Mapping problem with bowtie2 paremeter --very-sensitive and --very-sensitive-local
mapping
soil
microbiome
metagenomic
1 day ago by
hophuquy0944
• 0
1
vote
3
replies
141
views
Unable to register for MG-RAST
metagenomics
MG-RAST
updated 21 hours ago by
GenoMax
146k • written 1 day ago by
naveedhasan2000
▴ 10
0
votes
0
replies
92
views
Comparing GSEA mutant data to wild type
python
gene
GSEA
R
1 day ago by
conmul
• 0
0
votes
1
reply
161
views
GATK BaseQualityRecalibrator
SNPs
BQSR
variants
reads
gatk
updated 1 day ago by
LChart
4.3k • written 1 day ago by
ayeraselvan
▴ 10
0
votes
0
replies
97
views
Duplicates in TCGAanalyze_Normalization
R
TCGAanalyze_Normalization
TCGAbiolinks
studio
1 day ago by
Azra
▴ 10
4
votes
3
replies
331
views
Selecting DEGs for gene ontology using clusterprofiler and DESeq2
R
DESeq2
RNAseq
13 hours ago by
a.basitkhan1990
▴ 60
0
votes
6
replies
282
views
Has this sequence really more then 70k perfect matches in the human genome?
BLAST
updated 1 day ago by
i.sudbery
20k • written 1 day ago by
gernophil
▴ 90
0
votes
0
replies
116
views
Long non-coding RNA target
target
gene
lncRNA
2 days ago by
zizigolu
★ 4.3k
0
votes
2
replies
203
views
Alternative to RDP
taxonomy
rdp
updated 1 day ago by
GenoMax
146k • written 3 days ago by
asdata
• 0
0
votes
0
replies
109
views
News:
Multivariate Data Analysis with R and vegan course
Multivariate
Ordination-Methods
PCA
PCoA
2 days ago by
carlopecoraro2
★ 2.6k
0
votes
0
replies
111
views
Download serum miRNA data from TCGA
miRNA
Serum
download
TCGA
2 days ago by
fatemekazemi446
• 0
0
votes
0
replies
109
views
Tutorial:
How CCA alignment and cell label transfer work in Seurat
biology
computational
seurat
bioinformatics
scRNAseq
2 days ago by
Ming Tommy Tang
★ 4.4k
0
votes
0
replies
132
views
Refseq1405.40 and hisat2-build (-ss and --exon)
hisat2-build
updated 1 day ago by
GenoMax
146k • written 2 days ago by
chrisk
• 0
0
votes
0
replies
145
views
identify transposable elements in iso-seq data
TE
iso-seq
RepeatMasker
1 minute ago by
triplee0305
▴ 10
0
votes
1
reply
187
views
Job:
Freelance Tutor for Mouse Gene Comparison
Mouse
updated 1 day ago by
Dunois
★ 2.7k • written 2 days ago by
yourgoodnabor
• 0
1
vote
3
replies
234
views
Why higher read counts in chromosome M/MT
IGV
MT-DNA
count
mitochondria
read
updated 2 days ago by
ATpoint
85k • written 2 days ago by
Lou11
• 0
0
votes
1
reply
163
views
Issue with longqc conda installation
longqc
updated 1 day ago by
GenoMax
146k • written 2 days ago by
Daniele
• 0
0
votes
0
replies
133
views
scRNA seq disssimlarity plot
anosim
scRNA-seq
dissimilarity
2 days ago by
carolofharvest
▴ 40
0
votes
0
replies
134
views
MOFA2: Confidence Intervals // Unvertainty estimates for MOFA model
Biostatistics
MOFA2
2 days ago by
mario_de_manner
▴ 20
0
votes
0
replies
152
views
How to extract the missing feature ( gene, CDS, ... when compare 2 gff3 file ?
gff3
compare
MAKER
annotation
RAP-DB
3 days ago by
Sony
▴ 10
2
votes
9
replies
625
views
7 follow
How to determine whether it is 10x data
GEO
10x
SRA
updated 2 days ago by
LChart
4.3k • written 8 days ago by
king
• 0
0
votes
0
replies
152
views
DROP - Detection of RNA Outliers Pipeline
aberrantExpression
outlierDetection
DROP
BulkRNASeq
3 days ago by
Maverick
▴ 10
0
votes
1
reply
203
views
HISAT2 human index and GTF file version incompatibility
index
HISAT2
GTF
updated 3 days ago by
pinheirofabiano
▴ 90 • written 3 days ago by
Rituriya
▴ 40
0
votes
3
replies
339
views
alignment to human transcriptome with Bowtie2
alignment
updated 19 hours ago by
swbarnes2
14k • written 4 days ago by
Meghan.T
• 0
1
vote
1
reply
196
views
mappability regions
mappability
region
updated 3 days ago by
Alex Reynolds
35k • written 3 days ago by
heureuse
• 0
0
votes
0
replies
144
views
News:
Join Our Landscape Genomics Workshop in Lodz, Poland – January 20-24, 2025
Sambada
Data-Integration
Landscape-Genomics
3 days ago by
carlopecoraro2
★ 2.6k
119,305 results • Page
1 of 2387
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Comment: Gatk haplotyper
Answer: Question about edgeR p-values/FDR values
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Comment: Best practices in Fungal Genome Assembly
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Answer: Pseudobulk analysis using AggregateExpression()
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Comment: Question about edgeR p-values/FDR values
by
dariober
15k
+1, in particular for this: > The fact that you want a p-value for each sample, suggests to me that the question you are trying to answer …
Comment: Spades Genome Assembly
by
dthorbur
★ 2.5k
I assume this is a similar issue to [this post](https://www.biostars.org/p/9555060/). The `--isolate` flag expects high coverage and qualit…
Answer: Question about edgeR p-values/FDR values
by
i.sudbery
20k
edgeR will only ever give one P-value/FDR per gene - the P-value/FDR for the contrast you asked it about. In your LRT, you set the group to…
Comment: Question about edgeR p-values/FDR values
by
Ronin
▴ 10
Got it. Thank you for describing it that way, when I think about it as a sophisticated t-test it makes total sense to me why we get one p-v…
Comment: Question about edgeR p-values/FDR values
by
dariober
15k
> Where we have P-values and FDR values at every ATAC-seq region for each of the 18 samples. What do you think? No, that doesn't make sens…
Comment: Gatk haplotyper
by
Michael
55k
If you think of the tumor under an infinite sites model, then yes, all germline variants will be present in the tumor. However, it isn't at…
Comment: Question about edgeR p-values/FDR values
by
Ronin
▴ 10
I guess my advisor is expecting to see something like this in the edgeR_results.csv file: logFC logCPM LR sample1PValue sample1FDR sa…
Answer: Plot query cells on top of reference cells in UMAP
by
Bastien Hervé
5.7k
In the metadata of your Seurat object you know which cell is coming from the query or the reference. If you set this information in a colum…
Comment: Question about edgeR p-values/FDR values
by
dariober
15k
I don't understand where you expect to see the 18 samples? In the ouptut of topTags or in the PCA plot? The topTags will give one row per r…
Answer: Is it necessary to adjust genome to the same strand direction?
by
Xian
▴ 60
What are you using vg for? In general our tools will consider both strands so you shouldn't need to change the direction
Comment: VG giraffe autoindex and alignement mapping warning "Refusing to perform too-lar
by
Xian
▴ 60
No, it shouldn't be a problem. It's missing just one read out of the whole set, and for this one its mate pair was mapped so you'll still h…
Comment: Pseudobulk analysis using AggregateExpression()
by
Bastien Hervé
5.7k
I don't know how to explain myself better, please read again my comment on normalization by the total number of transcripts in each meta ce…
Comment: Gatk haplotyper
by
prs
▴ 20
Ok. I was going with this approach only, but I thought it would be a kind of checkpoint to see variants in tumor bam also, as a germline va…
Comment: Question about edgeR p-values/FDR values
by
Ronin
▴ 10
Hi, thanks for the comment. My suspicion is that what you said here: > Maybe there is a bit of confusion about the word sample here (in > …
Comment: Question about edgeR p-values/FDR values
by
Ronin
▴ 10
(Part 2) library(edgeR) dge <- DGEList(counts = count_data, group = groups$tissue) print(dge) table(groups$tissue) …
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