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119,052 results • Page
1 of 2382
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Forum:
How to work with Low allele Depth Variants in Strelka Variant caller
allelic
bioinformatics
strelka
depth
low-GQX
10 minutes ago by
abhishekghadge
▴ 30
0
votes
1
reply
741
views
What is the meaning of 'a too large, ITMAX too small in gamma countinued fraction (gcf)'
meta-analysis
METAL
GWAS
updated 1 hour ago by
Ram
44k • written 18 months ago by
ymberzal
• 0
0
votes
0
replies
1.4k
views
METAL meta-analysis software crash
metal
meta-analysis
gwas
updated 1 hour ago by
Ty
• 0 • written 4.5 years ago by
ydadmehr
• 0
0
votes
1
reply
43
views
Question on batch effect for a bulk RNA seq analysis
RNA-seq
batch-effect
updated 1 hour ago by
Ram
44k • written 2 hours ago by
akb
• 0
1
vote
3
replies
110
views
cutadapt not working when calling in a bash code with qsub
qsub
trim
cutadpat
updated 3 hours ago by
ATpoint
85k • written 6 hours ago by
Meghan.T
• 0
2
votes
3
replies
110
views
Removing features from RNA assay in seurat
R
SEURAT
sc-RNA-Seq
updated 6 hours ago by
yura.grabovska
▴ 510 • written 7 hours ago by
Varun Gupta
★ 1.3k
0
votes
0
replies
45
views
News:
Eukaryotic Genome Assembly Using PacBio and Hi-C course (4-8 November)
Genome-Assembly
PacBio
Long-reads
Hi-C
7 hours ago by
carlopecoraro2
★ 2.6k
0
votes
6
replies
857
views
miRNAseq - over-presented sequence in negative control
miRNAseq
adaptor
dimer
updated 7 hours ago by
Ant
▴ 10 • written 13 months ago by
MH85
▴ 20
819
votes
169
replies
156k
views
110 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 21 days ago by
Biostar
3.0k • written 7.8 years ago by
Istvan Albert
101k
0
votes
0
replies
56
views
News:
Online Workshop - Bioinformatics Pipeline Development with Nextflow (November 13-15, 2024)
Workshop
Nextflow
RNA-Seq
7 hours ago by
ecSeq Bioinformatics
• 0
0
votes
0
replies
45
views
Differential expression analysis from .chp files with Limma
expression
limma
IonTorrent
differential
8 hours ago by
Rogerio Ribeiro
▴ 110
0
votes
1
reply
171
views
Genome Polishing nextPolish
nextpolish2
nextpolish
pilon
racon
updated 8 hours ago by
shelkmike
★ 1.3k • written 2 days ago by
Umer
▴ 110
0
votes
1
reply
147
views
co-occurrence matrix from my VCF file
co-occurrence
vcf
updated 8 hours ago by
robben
• 0 • written 1 day ago by
HarperReed
• 0
2
votes
6
replies
1.6k
views
Center multiple pheatmap
pheatmap
patchwork
updated 8 hours ago by
yura.grabovska
▴ 510 • written 3.8 years ago by
5utr
▴ 370
3
votes
3
replies
167
views
creat histogram in R
R
ggplot2
hist
updated 9 hours ago by
Ram
44k • written 15 hours ago by
G.S
▴ 60
2
votes
2
replies
127
views
constructing gene-based pangenome from orthofinder output file
orthofinder
pan-genome
7 hours ago by
analyst
▴ 50
3
votes
6
replies
280
views
Genome Assembly Sorting
genome
assembly
sorting
updated 1 day ago by
GenoMax
146k • written 1 day ago by
Umer
▴ 110
0
votes
3
replies
213
views
Install PacBio lima via conda fails
conda
updated 16 hours ago by
colindaven
6.8k • written 1 day ago by
michael.flower.14
▴ 200
1
vote
3
replies
157
views
human_variation_vcf
BaseRecalibrator
14 hours ago by
runfreely2
• 0
2
votes
2
replies
172
views
How to interpret Eigengene dendrongram results
Eigengene
dendrogram
6 hours ago by
nuorain
▴ 20
6
votes
23
replies
1.6k
views
GTF file
cellranger-arc
GTF
cellranger-arc-2.0.2
updated 14 hours ago by
Michael
55k • written 6 weeks ago by
IrK
▴ 90
0
votes
4
replies
199
views
Explanation of DESeq factor leveling
DESeq
3 hours ago by
bthom
• 0
0
votes
0
replies
92
views
batch correction limma package (bead based assay data)
batch-correction
updated 1 day ago by
Ram
44k • written 1 day ago by
maria jose
• 0
0
votes
1
reply
119
views
Allele frequency plot : imputed vs reference panel variants
imputation
genotyping
reference
updated 11 hours ago by
BlastedBadger
▴ 160 • written 1 day ago by
hello_genome
• 0
0
votes
1
reply
134
views
rRNA contamination after filtering
QC
contamination
ribosomal-RNA
updated 21 hours ago by
GenoMax
146k • written 1 day ago by
sleepystudent
• 0
1
vote
0
replies
89
views
Repeated ensembl IDs in microarray DEG analysis
R
annotation
DEGs
microarray
limma
1 day ago by
Pereira G
▴ 10
0
votes
2
replies
219
views
How to filter annotated genes overlapping with TE/repeat element?
genome
gene
annotation
14 hours ago by
Yao
▴ 30
24
votes
13
replies
540
views
6 follow
Forum:
How to do datamining in bioinformatics
data-mining
updated 6 hours ago by
LauferVA
4.5k • written 1 day ago by
Biomed-jeh
▴ 60
2
votes
3
replies
2.2k
views
Why parametric linkage analysis on Merlin gives zero "0" LOD score?
SNP
alohomora
merlin
updated 1 day ago by
Ram
44k • written 6.5 years ago by
eDNAuRNA
▴ 20
0
votes
0
replies
101
views
fragment size estimation during vg mpmap and rpvg
vg
1 day ago by
Juhyun
• 0
0
votes
4
replies
238
views
WGCNA package.
RNA-seq
WGCNA
1 day ago by
Jaber
▴ 20
1
vote
1
reply
166
views
Single-cell RNA differential expression with an unbalanced number of cells between conditions
single-cell
differential-expression
updated 1 day ago by
jared.andrews07
★ 17k • written 1 day ago by
Javi.villegas21
• 0
0
votes
1
reply
133
views
What are the epithelial cells subtype in esophagus tissue ?
python
scanpy
anndata
single-cell
updated 1 day ago by
ATpoint
85k • written 1 day ago by
JACKY
▴ 160
0
votes
0
replies
107
views
News:
ONLINE COURSE – Genome Assembly and Annotation (GAAA01)
Annotation
Genome
Assembly
Genomics
updated 1 day ago by
GenoMax
146k • written 1 day ago by
oliverhooker
▴ 110
0
votes
1
reply
131
views
News:
Course: Single-cell RNA-seq analysis with R/Bioconductor
Bioconductor
single-cell-RNAseq
updated 1 day ago by
yura.grabovska
▴ 510 • written 1 day ago by
carlopecoraro2
★ 2.6k
0
votes
0
replies
102
views
Query regarding variant calling (SVs) using vg giraffe workflow
pangenome
giraffe
vg
1 day ago by
s_135
▴ 10
3
votes
2
replies
426
views
Query about vg (and vg giraffe) for pangenome creation and VC
pangenome
giraffe
vg
1 day ago by
s_135
▴ 10
2
votes
4
replies
199
views
GSVA with a genelist on a "per-cluster" basis
GSVA
scRNA-seq
genelist
1 day ago by
bio_info
▴ 20
0
votes
0
replies
97
views
Checking Sequence Duplication or errors in a de novo transcriptome assembly
DuplicatedSequences
assemblyError
redundantSequences
deNovoTranscriptome
1 day ago by
Vin Dee
• 0
0
votes
0
replies
87
views
Pausin index for qpro-seq
pausing
qpro-seq
index
1 day ago by
daffodil
▴ 10
1
vote
2
replies
156
views
Selecting appropriate expressed repeat annotation for Velocyto
velocyto
repeatmasker
scRNAseq
1 day ago by
merdanosman
• 0
0
votes
1
reply
148
views
Regions got skipped due to length
Getfasta
Bedtools
updated 1 day ago by
Pierre Lindenbaum
164k • written 1 day ago by
Muhammad
• 0
1
vote
10
replies
370
views
Using a different reference transcriptome assembly from different RNA seq libraries (but same species)
TranscriptomeAssembly
Libraries
17 hours ago by
Vin Dee
• 0
2
votes
3
replies
237
views
Error function vst in DESeq2
vst
DESeq2
updated 1 day ago by
yura.grabovska
▴ 510 • written 2 days ago by
Larissa
• 0
0
votes
3
replies
244
views
Tumor purity in TCGA data analysis
TCGA
tumor-purity
updated 1 day ago by
Ram
44k • written 2 days ago by
nuorain
▴ 20
0
votes
0
replies
133
views
Help with EIGENSOFT's SmartPCA
SmartPCA
EIGENSOFT
PCA
2 days ago by
Junaid
• 0
0
votes
0
replies
123
views
Matching of GSVA score of a single sample to its drug sensitivity
GSVA
2 days ago by
marionette.kent
• 0
0
votes
1
reply
264
views
Software For MHC Typing Using Mouse NGS (WES or RNAseq)?
MHC
updated 2 days ago by
mourisl
▴ 30 • written 8 days ago by
kilcdincer
▴ 10
2
votes
1
reply
279
views
DMRCate mean diff values
design
methylation
dmrcate
updated 2 days ago by
james.hawley
▴ 70 • written 5 days ago by
Eren
• 0
0
votes
1
reply
182
views
Looking for any study/research paper that used gcPathogen database
gcPathogen
updated 1 day ago by
GenoMax
146k • written 2 days ago by
Albert
• 0
119,052 results • Page
1 of 2382
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Comment: Using samtools with GCS (google cloud storage) on a docker container seems to gi
Answer: Using samtools with GCS (google cloud storage) on a docker container seems to gi
Comment: Center multiple pheatmap
Answer: cutadapt not working when calling in a bash code with qsub
A: Limiting memory usage aligner MAFFT uses
Limiting memory usage aligner MAFFT uses
Comment: Removing features from RNA assay in seurat
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Recent Replies
Comment: Question on batch effect for a bulk RNA seq analysis
by
Ram
44k
Please use the formatting bar (especially the `code` option) to present your post better. You can use backticks for inline code (\`text\` b…
Comment: What is the meaning of 'a too large, ITMAX too small in gamma countinued fractio
by
Ram
44k
"I have the same problem" is not an answer, why add it as one? Use `Add Comment` instead. I've moved it this time.
Comment: Explanation of DESeq factor leveling
by
bthom
• 0
I am not sure that I follow, factors in R are stored as integers with labels assigned to them. Furthermore, the code example in the DESeq v…
Comment: cutadapt not working when calling in a bash code with qsub
by
ATpoint
85k
Please show full script and replace the single by double quotes so the variable can expand.
Comment: cutadapt not working when calling in a bash code with qsub
by
Meghan.T
• 0
So, > no such file or directory: '${trimmed_dir}/r1.fq refers to the output of the cutadapt. since cutadapt did not work , the script co…
Answer: cutadapt not working when calling in a bash code with qsub
by
Pierre Lindenbaum
164k
> no such file or directory: '${trimmed_dir}/r1.fq it looks like you escaped a dollar sign in your script. The variable is not replaced …
Comment: Explanation of DESeq factor leveling
by
swbarnes2
14k
I assume the difference in whether factor was used isn't doing anything because the elements of MFG are strings, and not numbers?
Comment: How to interpret Eigengene dendrongram results
by
nuorain
▴ 20
Thank you so much for your reply.
Comment: How to do datamining in bioinformatics
by
LauferVA
4.5k
thanks for this - will help a collaborator and I !!
Comment: How to do datamining in bioinformatics
by
LauferVA
4.5k
yeah. ingenuity's knowledge base (what i understand of it, anyway) is incredible, but ive not looked into analysis match. i'll take a peek …
Comment: Explanation of DESeq factor leveling
by
bthom
• 0
Hm, thanks for the insight. It seems like both the fold changes and the padj are slightly different. Can you explain how the choice of the …
Comment: Removing features from RNA assay in seurat
by
yura.grabovska
▴ 510
In your code: obj[["RNA"]] <- subset(obj[["RNA"]], features = setdiff(rownames(obj[["RNA"]]), antibody_capture_genes)) This shouldn't…
Comment: Removing features from RNA assay in seurat
by
Varun Gupta
★ 1.3k
What happens to the HTO assay?
Comment: Removing features from RNA assay in seurat
by
yura.grabovska
▴ 510
I probably wouldn't recommend doing this, but anyway: You can subset the assay rather than the whole object test.seurat[["RNA2"]] <- …
Comment: How to do datamining in bioinformatics
by
jared.andrews07
★ 17k
The [recount project](https://jhubiostatistics.shinyapps.io/recount3-study-explorer/) is an admirable free alternative.
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