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867 results • Page
6 of 18
Sort: Views
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Views
Votes
Replies
0
votes
0
replies
741
views
Creating a stable batch-corrected scRNA-Seq data with multiple datasets and multiple integrations
RNA-Seq
scRNA-Seq
batch-effect
updated 28 days ago by
Ram
43k • written 3.5 years ago by
hkarakurt
▴ 180
0
votes
0
replies
739
views
"No group or design set" with deAna() function in EnrichmentBrowser package
RNA-Seq
R
EnrichmentBrowser
updated 29 days ago by
Ram
43k • written 4.1 years ago by
yxswhx
• 0
1
vote
6
replies
722
views
anRichment is missing
WGCNA
anRichment
updated 10 days ago by
GenoMax
142k • written 6 months ago by
michael.flower.14
▴ 180
2
votes
4
replies
719
views
Count all variants from vcf file
variants
vcf
Count
updated 9 days ago by
Pierre Lindenbaum
161k • written 21 months ago by
t.ali
• 0
5
votes
4
replies
716
views
DEG analysis of RNA-seq data across multiple tissues and two conditions
RNA-seq
EdgeR
DEGs
DESeq2
28 days ago by
BioinfGuru
★ 1.7k
5
votes
4
replies
711
views
How to compare the quality of assemblies
nextdenovo
assembly
hifiasm
pacbio
22 days ago by
kirillkirilenko
▴ 40
0
votes
11
replies
709
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo
scRNA-seq
STAR
snRNA-seq
MGI
20 days ago by
atowns21
• 0
0
votes
1
reply
700
views
after selecting specific GO terms to plot, cneplot is not showing any color for genes, GO terms and only showing lines without nodes.
cneplot
updated 15 days ago by
Ram
43k • written 15 days ago by
Dr Huma Naz
• 0
0
votes
3
replies
696
views
Pluritest for pluripotency broken
pluripotent
pluritest
cells
stem
updated 7 days ago by
DGTool
▴ 20 • written 21 months ago by
yassine
• 0
3
votes
10
replies
693
views
Piping samtools to R
R
NGS
bash
samtools
29 days ago by
noodle
▴ 580
2
votes
9
replies
689
views
Filtering Multi-sample VCF file for all except one Genotype
variant
SNP
VCF
updated 1 day ago by
Pierre Lindenbaum
161k • written 9 days ago by
schmince
• 0
1
vote
0
replies
681
views
Conditions for valid batch effect correction
r
batch-effect
updated 29 days ago by
Ram
43k • written 5.2 years ago by
Sebastian Hesse
▴ 340
3
votes
8
replies
678
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 10 days ago by
Chris Dean
▴ 410 • written 14 days ago by
sovrappensiero
▴ 100
1
vote
1
reply
667
views
Save experiment with batch effects - Protein microarray
statistics
protein-array
batch-effect
updated 29 days ago by
Ram
43k • written 4.4 years ago by
s.lima.diogenes
▴ 10
6
votes
8
replies
665
views
BRAKER3 genome annotation
annotation
BRAKER3
genome
updated 29 days ago by
dariober
14k • written 4 weeks ago by
manaswiniparija3
▴ 40
1
vote
5
replies
665
views
Duplicate marking, read names, and the SRA
SRA
MarkDuplicates
updated 27 days ago by
GenoMax
142k • written 27 days ago by
Luka
• 0
5
votes
5
replies
659
views
Tutorial:
how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix
RNAseq
R
updated 13 days ago by
Mbofire
• 0 • written 21 days ago by
Ming Tommy Tang
★ 3.9k
0
votes
4
replies
655
views
Per base sequence content failed miserably
fastqc
sequence
trimmomatic
NGS
assembly
27 days ago by
Kai Xin
• 0
0
votes
1
reply
654
views
Job:
Seeking Bioinformatics/Drug Design Opportunities - PhD in Pharmacology with Experience in RNA-seq, CADD & Deep Learning Molecular Generation
search
job
updated 11 days ago by
GenoMax
142k • written 11 days ago by
tulip
• 0
2
votes
2
replies
646
views
Batch correction for DE analysis
batch-correction
mRNA
RNA-seq
DEGs
MDSplot
updated 29 days ago by
Ram
43k • written 2.7 years ago by
Yoonji
▴ 10
1
vote
5
replies
640
views
Cell barcode whitelists for DNBelab C Series High-throughput Single-cell RNA Series Library Preparation Set?
cell-barcode
MGI
DNBelab
single-cell
updated 23 days ago by
atowns21
• 0 • written 3 months ago by
benjamin.pyenson
• 0
3
votes
5
replies
632
views
SLURM submission problem: Indexing the Reference Genome is not done in STAR
align
RNA-Seq
linux
STAR
24 days ago by
n_navy
• 0
0
votes
7
replies
631
views
Post-imputation plot
michigan-imputation-server
quality-control
updated 13 days ago by
LChart
3.9k • written 17 days ago by
kl
▴ 10
2
votes
5
replies
631
views
MEGA Analysis Issue on High-Performance Computer
phylogenetic-analysis
MEGA
updated 25 days ago by
Mensur Dlakic
★ 27k • written 27 days ago by
Giorgio
• 0
4
votes
7
replies
631
views
Very low RNA splicing rate for pulmonary AT2 cells
RNA-velocity
scVelo
scRNA-seq
splicing
17 days ago by
e.r.zakiev
▴ 210
3
votes
1
reply
627
views
What is the normalization status of metabric data?
metabric
normalization
microarray
cbioportal
updated 28 days ago by
etiennedanis
▴ 20 • written 20 months ago by
DareDevil
★ 4.3k
0
votes
4
replies
616
views
how to find genes that are significantly expressed in brain cortex samples
rna-seq
gene-expression
updated 26 days ago by
ATpoint
82k • written 27 days ago by
rheab1230
▴ 140
3
votes
9
replies
611
views
Is it Acceptable to Have Uniform Quality Scores in a FASTQ File?
FASTQ
updated 22 days ago by
Istvan Albert
100k • written 24 days ago by
Κοσμάς
• 0
0
votes
10
replies
610
views
Low mapping rate with Salmon
RNA-seq
Salmon
Quantification
updated 16 days ago by
i.sudbery
19k • written 24 days ago by
Patadu94
• 0
1
vote
7
replies
607
views
ScRNA data question
scRNA
Vlnplot
Samples
updated 17 days ago by
bk11
★ 2.4k • written 21 days ago by
starswillfade
▴ 10
0
votes
0
replies
607
views
Differential accessibility using DiffBinf
diffbind
17 days ago by
Shloka
• 0
1
vote
7
replies
607
views
gvcf joint calling
WES
GATK
VCF
gVCF
18 days ago by
zihanss
• 0
4
votes
7
replies
604
views
To get p-values for the TPM
P-value
TPM
RSEM
updated 21 days ago by
dsull
★ 6.0k • written 22 days ago by
VITALA
• 0
0
votes
1
reply
602
views
Basic stats in hierfstat
Fst
stats
hierfstat
updated 14 days ago by
mdav
• 0 • written 19 months ago by
Zoe
• 0
0
votes
9
replies
594
views
Using VEP annotation output as the input for a second VEP annotation
Annotation
VEP
VCF
1 day ago by
Arton
▴ 10
0
votes
2
replies
593
views
How to get the reference panel for UKBB
UKBB
GWAS
clump
27 days ago by
航太郎
• 0
5
votes
6
replies
592
views
Programmatically retrieving positions of protein active site residues
Uniprot
PDB
Proteins
updated 16 days ago by
me
▴ 760 • written 17 days ago by
Mariana
▴ 40
0
votes
9
replies
589
views
Applying the metacell2 algorithm using python
python
single-cell
scanpy
metacell2
updated 1 day ago by
Wayne
★ 2.0k • written 10 days ago by
JACKY
▴ 140
0
votes
2
replies
587
views
autodockvina
python
python3
autodock
updated 28 days ago by
Ram
43k • written 4 months ago by
iamsmor
• 0
0
votes
0
replies
586
views
Correlation between cell type prediction scores and individual gene expression in spatial transcriptomic datasets
single-cell
Spatial-Transcriptomics
20 days ago by
biocellbio
• 0
7
votes
6
replies
586
views
Filtering sam or bam file with maximum matching region
crisper-edited
alignment
match
25 days ago by
analyst
▴ 50
3
votes
3
replies
579
views
Korean human genome reference file
GWAS
reference
imputation
27 days ago by
SeoGyun
• 0
0
votes
4
replies
577
views
How to reduce the variation of CIBERSORTx results?
CIBERSORTx
deconcolution
28 days ago by
feather-W
• 0
3
votes
8
replies
573
views
How to access TCGA samples that were treated with a specific drug?
TCGA
RNA-seq
10 days ago by
Qroid
▴ 40
2
votes
5
replies
569
views
Where to find the homopolymer regions bed file for Hg002 genome?
simple-repeats
hg002
bed
homopolymer-regions
29 days ago by
Bikram Kumar
• 0
2
votes
5
replies
564
views
Tissue-specific DEG analysis with DEseq2
DEseq2
RNA-seq
DEG
R
updated 4 days ago by
arctic
▴ 40 • written 13 days ago by
M.
▴ 30
1
vote
0
replies
561
views
The majority of the sequences in Trinity ID do not start from start codons. Can the sequences still be used for primer design and validation?
Primers
TRINITY
26 days ago by
mathavanbioinfo
▴ 90
0
votes
3
replies
561
views
JASPAR2024_getMatrixSet error
JASPAR2024
getMatrixSet
updated 7 days ago by
Ram
43k • written 12 weeks ago by
maplewj
▴ 10
0
votes
1
reply
560
views
HOMER on AWS
HOMER
updated 13 days ago by
clairechung112
• 0 • written 2.3 years ago by
Bogdan
★ 1.4k
0
votes
3
replies
554
views
python file for coding potential calculator
cpc2.py
updated 23 days ago by
atharvakarkare14
▴ 30 • written 28 days ago by
Ashok
• 0
867 results • Page
6 of 18
Recent Votes
ATAC-seq sample normalization
Answer: Faster Needleman-Wunsch rapid global alignment of two sequences?
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences?
Comment: Can I perform a correlation test with 3 biological replicates per condition?
Answer: --normalizeUsing RPGC
Answer: Details on salmon index
Answer: Details on salmon index
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Recent Replies
Comment: Merge clusters in Seurat UMAP
by
bk11
★ 2.4k
Can you try this? library(dplyr) seuratobj@meta.data <- seuratobj@meta.data %>% mutate(seurat_clusters = recode(seurat_clu…
Comment: Merge clusters in Seurat UMAP
by
kilcdincer
▴ 10
Thank you for the response but it does not change anything.
Comment: Merge clusters in Seurat UMAP
by
bk11
★ 2.4k
I have not tested but you could try something like below- seuratobj$seurat_clusters[seuratobj$seurat_clusters==5]=0 seuratobj$seur…
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences?
by
Gabriel R.
★ 2.9k
I know about it, isn't there a simple C++ static binary?
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences?
by
Gabriel R.
★ 2.9k
needle is great! but it does not handle sequences of 100k or so.
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
Ram
43k
Please use the formatting bar (especially the `code` option) to present your post better. You can use backticks for inline code (\`text\` b…
Comment: Single-cell ambient RNA correction: SoupX vs decontX contamination fraction
by
txema.heredia
▴ 130
The point is that you need to feed the ambient algorithm a clustering list as input. This way, it checks for genes present in the soup vs g…
Comment: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i
by
swbarnes2
14k
Wait, so the magnitudes of the PCs are in the thousands? That's not normal for RNASeq.
Comment: Help with VG Toolkit: VCF Output is Empty
by
Jordan M Eizenga
▴ 460
What do you get if you use `vg stats -a` on the GAM file?
Comment: About runing Pilon on individual chromosomes when polish draft genome assembly
by
sansan_96
▴ 90
Hello, What approach could you recommend for a large genome (3Gb) with about 10k scaffolds? I'm having problems with RAM when processing t…
Comment: Single-cell ambient RNA correction: SoupX vs decontX contamination fraction
by
e.r.zakiev
▴ 210
Very good question and analysis. I personally only tried SoupX so can't weigh in on the comparison. This might be not really the issue here…
Comment: Is there any way to modify this pie chart ?
by
marco.barr
▴ 120
Try following the same logic as the guide which adds the labels about halfway through each pie slice value. Check column's name in script b…
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
hophuquy0944
• 0
sorry for that, this is first time i use it.
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
hophuquy0944
• 0
thank sir, i will check it again
Comment: In one PCA plot, can I calculate the percentage of different factors that contri
by
diqixiaoyaoer
▴ 10
Ok, I will response to you here as soon as possible.
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