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778 results • Page
5 of 16
Sort: Views
Rank
Views
Votes
Replies
0
votes
4
replies
641
views
Can vg take MUMmer output as input?
vg
updated 5 hours ago by
Qi
• 0 • written 2.8 years ago by
ac2278
▴ 20
3
votes
6
replies
639
views
BWA | SAMtools | GATK debugging help
alignment
mapping
vcf
13 days ago by
TheScriptOfGilgamesh
▴ 20
2
votes
4
replies
637
views
Genome data visualization
gff3
bed
regions
genome
27 days ago by
polag01
▴ 10
8
votes
6
replies
637
views
Problems using ERCC spike-ins for normalization in DESeq2
Spike-ins
Differential-expression
DESeq2
RNA-seq
13 days ago by
manuel.fernandez
▴ 40
0
votes
4
replies
624
views
CAZy database has multiple family sequence...
metagenomics
cazy
annotation
updated 19 days ago by
JyiYeung
• 0 • written 9 months ago by
GYUDAE
• 0
0
votes
0
replies
623
views
How can I summarize Log2 Fold Change values for many genes within a treatment group?
fold-change
updated 10 days ago by
Ram
40k • written 2.4 years ago by
sagrant
▴ 10
0
votes
1
reply
611
views
RNAseq gene clustering. Silhouette results generation from the NMF consensus membership matrix using the R ‘cluster’ package
NMF
RNAseq
clustering
R
updated 26 days ago by
Hamid Ghaedi
3.0k • written 16 months ago by
Leo
• 0
0
votes
4
replies
605
views
CDHIT para and cdhit slow speed
processing
cdhit-para
DNA
cdhit
updated 29 days ago by
meyezili
• 0 • written 10 weeks ago by
ahteshamabbasi1996
▴ 10
13
votes
10
replies
605
views
8 follow
scRNAseq Differential expression analysis
scRNA-seq
Differential-Expression
Seurat
updated 1 day ago by
ATpoint
76k • written 4 days ago by
MVJ
▴ 10
3
votes
7
replies
601
views
GATK AnnotateVcfWithBamDepth returns zero DP for all variants in VCF
GATK
AnnotateVcfWithBamDepth
27 days ago by
ClkElf
▴ 50
2
votes
3
replies
600
views
How to change standard genetic code in Artemis?
Mycosplasma
Artemis
updated 4 days ago by
Ram
40k • written 2.8 years ago by
A_heath
▴ 140
1
vote
9
replies
600
views
more reads in metagenomic samples after 'removing host reads'
bowtie2
samtools
updated 10 days ago by
GenoMax
134k • written 11 days ago by
sapuizait
▴ 10
0
votes
0
replies
593
views
Contig extension using PRICE
price
updated 4 days ago by
Ram
40k • written 3.0 years ago by
A_heath
▴ 140
0
votes
7
replies
592
views
What is wrong with my NCBI esearch command for 16S rRNA?
16S
NCBI
Entrez
assembly
updated 10 days ago by
GenoMax
134k • written 12 days ago by
Morgan S.
▴ 80
4
votes
5
replies
591
views
Help with error scanpy
scanpy
12 days ago by
Chris
▴ 180
1
vote
6
replies
591
views
Found some plasmids in my sequence. IS there any tool or process by which i can find whether there are any AMR genes within those sequence?
WGS
updated 27 days ago by
Ram
40k • written 28 days ago by
Mustafa
• 0
1
vote
8
replies
591
views
NCBI Gene Table Bulk Download
ncbi
gene_table
updated 14 days ago by
GenoMax
134k • written 17 days ago by
fafad046
• 0
3
votes
7
replies
587
views
Nextflow - How to pass the yml format input file from an argument to channel as a list
python
groovy
yaml
nextflow
13 days ago by
kani
▴ 10
2
votes
3
replies
586
views
What is the fastest nucleotide sequence alignment search tool for 100mer queries versus a 2G database for nearly similar matches
alignment
read
nucleotide
aligner
sequence
updated 14 days ago by
GenoMax
134k • written 15 days ago by
a615ebfb
▴ 30
0
votes
0
replies
584
views
Job:
Research Technician II - Psychiatry
Research-Technician
Washington-University
Alzheimers
Dementia
updated 12 days ago by
Ram
40k • written 8 months ago by
Christi
• 0
4
votes
7
replies
583
views
Help with Error: None of the requested features were found: PECAM1 in slot data
seurat
multiome
26 days ago by
Chris
▴ 180
0
votes
5
replies
574
views
Bowtie2 with secondary alignment option produces multiple mapping with offset and varying alignment scores
bowtie2
score
alignment
multiple-alignment
22 days ago by
polag01
▴ 10
1
vote
6
replies
574
views
Batch correction in DESeq2 - limited impact for unsupervised downstream analyses
deseq2
13 days ago by
Jane
• 0
1
vote
8
replies
572
views
Negative Expression in RNA Assay on Dot Plot After SCT Transform
scttransform
scrnaseq
merge
Normalization
scaledata
updated 25 days ago by
fracarb8
★ 1.2k • written 26 days ago by
Kazo
• 0
1
vote
0
replies
570
views
Tool:
Mabs, a parameter optimizer for Hifiasm and Flye
assembly
9 days ago by
shelkmike
▴ 980
1
vote
6
replies
567
views
How to use the Combat-seq for batch effect removal?
batch-effect
normalization
Combat-seq
updated 27 days ago by
Ram
40k • written 29 days ago by
Yoomi
• 0
1
vote
2
replies
565
views
Cellchat log fold change
scRNA-seq
Fold-change
LRinteraction
CCI
cellchat
updated 10 days ago by
Ram
40k • written 10 weeks ago by
miyeok
• 0
0
votes
2
replies
565
views
News:
The Practice of RADseq: Population Genomics Analysis with Stacks (RADS02) Early bird deadline approaching - 20th September
population-genomics
radseq
stacks
updated 6 days ago by
Dave Carlson
★ 1.4k • written 7 days ago by
oliverhooker
▴ 110
10
votes
8
replies
563
views
Adding a control sample to bulk RNA-seq
RNA-seq
4 days ago by
Chris
▴ 180
3
votes
7
replies
562
views
Identifying transcription factors for a list of genes
transcription-factor
updated 12 hours ago by
Ram
40k • written 28 days ago by
lbombini
• 0
5
votes
4
replies
560
views
How to correct a wrong protein extraction from FASTA file?
fasta
bash
updated 4 days ago by
Ram
40k • written 3.1 years ago by
A_heath
▴ 140
0
votes
2
replies
556
views
module and trait correlation for WGCNA
treatment
WGCNA
relation
microarray
module-treatment
updated 6 days ago by
AS-git
• 0 • written 6 months ago by
Shriyansh
• 0
0
votes
2
replies
554
views
Network analysis for two Factors
chip-seq
network-analysis
updated 24 days ago by
Ram
40k • written 7 months ago by
Ankit
▴ 390
4
votes
8
replies
553
views
Assistance with Fungal Genome Annotation Using Maker and BLAST
gff3
fasta
maker
xml
blastp
1 day ago by
Edoardo
• 0
6
votes
5
replies
551
views
Can BWA (mem) detect longer deletions?
alignment
bwa
updated 14 days ago by
ATpoint
76k • written 19 days ago by
weixiaokuan
▴ 140
0
votes
13
replies
549
views
STAR Intron Motif Script Gives Segmentation fault Error
STAR
Linux
2 days ago by
Y
• 0
1
vote
5
replies
547
views
CellRanger output more cells than specified using --force-cells? Why?
scRNA-seq
cellranger
20 days ago by
rohitsatyam102
▴ 750
0
votes
0
replies
547
views
after gatk VariantAnnotator -V *_com_norm.vcf -A AlleleFraction -O *_norm_AB.vcf There "nan,nan" or "nan" in my vcf file
gatk
AlleleFraction
VariantAnnotator
updated 6 days ago by
Ram
40k • written 7 days ago by
zhuo
• 0
5
votes
7
replies
547
views
Can one sample t.test be used to determine statistical significance for log2FC values?
log2FC
T.test
updated 26 days ago by
dsull
★ 4.7k • written 27 days ago by
aUser
▴ 30
2
votes
5
replies
546
views
6 follow
Forum:
Biostar as a next generation version
app
mobile
Biostar
software
tools
updated 27 days ago by
ATpoint
76k • written 27 days ago by
rj.rezwan
• 0
0
votes
6
replies
544
views
How to get top 10 genes expressed in a cluster ( for cell type identification)?
seurat
12 days ago by
Chris
▴ 180
1
vote
2
replies
543
views
convert bed12 to sorted gtf
bed12
gtf
gff
awk
updated 13 days ago by
alejandrogzi
▴ 30 • written 14 months ago by
maria
• 0
2
votes
5
replies
540
views
How to distinguish between normal and malignant epithelial cells based on CNV?
scRNA-seq
r
CNV
infercnv
CNA
updated 14 days ago by
LChart
3.3k • written 19 days ago by
fifty_fifty
▴ 60
4
votes
7
replies
538
views
How is the format of the bed file for samtools ampliconclip
samtools
ampliconclip
updated 20 days ago by
aw7
▴ 210 • written 24 days ago by
ManuelDB
▴ 70
0
votes
8
replies
532
views
Microarray DGE analysis
microarray
DGE
updated 27 days ago by
bk11
★ 1.2k • written 28 days ago by
bioinformatics
▴ 20
0
votes
6
replies
530
views
A cluster expresses two types of cells' markers in scRNA-seq
scRNA-seq
annotate
28 days ago by
feather-W
• 0
1
vote
1
reply
529
views
scanpy add metadata
scanpy
metadata
updated 11 days ago by
yl759
▴ 40 • written 11 weeks ago by
Andy
▴ 90
0
votes
9
replies
528
views
Large number of gaps at the beginning of alignments
clustal-omega
DNA
alignment
updated 11 days ago by
Ram
40k • written 11 days ago by
Pit
• 0
8
votes
6
replies
528
views
Short Read Data Genome Assembly
spades
genome-assembly
updated 16 days ago by
ccstaats
▴ 30 • written 19 days ago by
Umer
▴ 50
7
votes
6
replies
526
views
Best practices scRNA-seq guide for beginer
scRNA-seq
eBook
24 days ago by
octpus616
▴ 80
778 results • Page
5 of 16
Recent Votes
Comment: Calculation of TMB on gene level
Recommended way to normalize SmartSeq2 gene expression matrix to better match 10X expression data
Answer: Filter transcription factors
Comment: Quantification after transcriptome assembly with Trinity
Snakemake: output folder a as dependency to a different rule
A: Snakemake: output folder a as dependency to a different rule
A: In Seurat, How Do nCount_RNA Differ from nFeature_RNA?
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Recent Replies
Comment: bcftools error merging two VCFs: REF prefixes differ
by
iraun
6.1k
I can't find information with respect to the reference genome used to call the variants in `VCF_d`, but in `VCF_p` it seems they used GRCh3…
Comment: Calculation of TMB on gene level
by
smrutimayipanda
▴ 20
I am asking about TMB calculation on gene level, especially TCGA data
Comment: Calculation of TMB on gene level
by
smrutimayipanda
▴ 20
can you please tell me why it is technically incorrect?
Answer: Gene enrichment analysis of prokaryotes gene
by
dthorbur
▴ 550
[Here](https://github.com/golden75/prokaryote_RNASeq) is a tutorial on how to use the R package DESeq2 for prokaryotic RNAseq analyses. [H…
Comment: Read block operation failed with BAM file
by
John Marshall
3.0k
Indeed, though it is a seek issue when accessing files **over HTTP and other network protocols**. So, unless there's something you didn't m…
Comment: geom_signif() uses t-test to compare between more than 3 groups... Isn't this wr
by
RM123
▴ 10
Thank you for your help. I am comparing 4 groups, but as I have gene expression data I have a considerable number of boxplots to make. I fo…
Comment: gene correlations in between two groups
by
ATpoint
76k
And how should I know this? I cannot read minds, nor see your screen, data or anything. Please ask a good question with necessary details. …
Comment: gene correlations in between two groups
by
edus_bioinfo
▴ 40
Thanks. But they are already analyzed. Afaik it analyzes raw data. In my dataset for each gene there is score. I want to interpret the data…
Answer: GWAS phenotype
by
dthorbur
▴ 550
Hello again. Yes, you can conduct GWAS using binary trait data, but it comes with a whole suite of complications. See [this](https://ww…
Comment: geom_signif() uses t-test to compare between more than 3 groups... Isn't this wr
by
RM123
▴ 10
Hello Dariober, That seems like a good solution, however I'm pretty new to R. Could you tell me how I can do that?
Comment: how to create a loop in R
by
Nicolas Rosewick
10k
Not really a bioinformatics related question. Start by looking at R tutorial, there is plenty of them online e.g. : https://www.statmethods…
Comment: Violin plot (Monocle 3) - Troubleshooting
by
fracarb8
★ 1.2k
You did not add the screenshot.
Answer: BED files
by
Alex Reynolds
35k
Generically via `bedmap`: ``` bedmap --echo --echo-map --count exome.bed annotations.bed > answer.bed ``` The `annotations.bed` fil…
Comment: geom_signif() uses t-test to compare between more than 3 groups... Isn't this wr
by
dariober
14k
It seems to me that anova followed by HSD is a more sensible approach than applying independent t-tests. Granted this is the first time I s…
Comment: BED files
by
barslmn
★ 1.8k
I am guessing you want the annotation files. https://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh38_latest/refseq_identifiers/
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