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43 results • Page
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76
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72
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19 follow
Tutorial:
Clustering of DAVID gene enrichment results from gene expression studies
enrichment
david
18 hours ago by
Kevin Blighe
87k
1
vote
8
replies
733
views
Adding CB tag to bam file
samtools
bam
updated 12 hours ago by
Pierre Lindenbaum
161k • written 6 days ago by
Maria
• 0
3
votes
8
replies
461
views
PCA plot (Suggestions Needed)
DESeq2
PCAplot
updated 15 hours ago by
swbarnes2
14k • written 1 day ago by
Aaliya
▴ 10
4
votes
7
replies
384
views
To get p-values for the TPM
P-value
TPM
RSEM
updated 12 hours ago by
dsull
★ 5.8k • written 1 day ago by
VITALA
• 0
7
votes
7
replies
5.9k
views
6 follow
How to know synonymous and non-synonymous SNPs from transcriptome sequencing
RNA-Seq
SNP
updated 4 hours ago by
rohitsatyam102
▴ 850 • written 6.1 years ago by
smallfish
▴ 10
2
votes
6
replies
3.6k
views
Treatment VS Control in Single Cell RNAseq analysis
Single Cell
RNAseq
DE Analysis
Treatment
Control
updated 39 minutes ago by
ATpoint
82k • written 3.9 years ago by
grayapply2009
▴ 280
0
votes
5
replies
260
views
Is it possible to get a list of representative genomes from a past RefSeq release?
representative
ncbi
asembly
refseq
updated 7 hours ago by
GenoMax
141k • written 1 day ago by
Bertalan_Takacs
▴ 90
3
votes
4
replies
155
views
Why gatk VariantAnnotator required bam and coverage files
gatk
VariantAnnotator
1 hour ago by
QX
• 0
2
votes
4
replies
2.3k
views
How could I generate a gi_taxid_nucl.dmp file similar to the one previously hosted by NCBI?
ncbi
metagenomics
centrifuge
gi_taxid_nucl.dmp
taxonomy
updated 16 hours ago by
ZhangYuanfeng
• 0 • written 2.4 years ago by
Frazier Baker
• 0
2
votes
4
replies
201
views
Fetch table from clinvar database according to a list of rsid
python
clinvar
perl
updated 10 minutes ago by
Ram
43k • written 14 hours ago by
ashaneev07
▴ 20
0
votes
4
replies
2.6k
views
Lositan freezing when generating selection table
LOSITAN
updated 18 hours ago by
evawillms183
• 0 • written 8.3 years ago by
andrepleao
• 0
0
votes
4
replies
234
views
different FeatureCounts output for the same data
fpkm
Counts
Rsubread
rna-seq
12 hours ago by
sehriban.buyukkilic
▴ 10
2
votes
3
replies
162
views
Figures are disappeared from html report of SnpEff
HTML
SnpEff
updated 9 hours ago by
Pierre Lindenbaum
161k • written 13 hours ago by
analyst
▴ 30
3
votes
3
replies
2.3k
views
How to make a TSS enrichment plot in ATAC-seq analysis?
ATAC
updated 6 hours ago by
sp
• 0 • written 22 months ago by
Dan
▴ 180
0
votes
3
replies
267
views
Heatmap and rna-seq
RNA-Seq
Heatmap
updated 10 minutes ago by
Ram
43k • written 2 days ago by
qudrat.nii
▴ 10
0
votes
2
replies
166
views
Creating Synthetic Sequences for a ML Model
DNA
ML
updated 22 hours ago by
Mensur Dlakic
★ 27k • written 1 day ago by
biochugs
• 0
14
votes
2
replies
7.0k
views
Trouble with Pilon installation
polishing
pilon
installation
updated 22 hours ago by
Lissa Cruz Saavedra
• 0 • written 7.3 years ago by
Rox
★ 1.4k
0
votes
2
replies
573
views
Why cd-hit-est not work when sequence identity threshold<0.95?
genome
cluster
sequence
updated 18 hours ago by
Dateline
• 0 • written 21 months ago by
JZX
• 0
1
vote
2
replies
180
views
alignment result
RNA-seq
samtools
hisat2
14 hours ago by
ahmad.sajad4541
• 0
2
votes
2
replies
76
views
Sequence read length shorter than flow cell specification
illumina
NGS
sequencing
updated 3 hours ago by
GenoMax
141k • written 4 hours ago by
M
• 0
1
vote
2
replies
103
views
ScRNA data question
scRNA
Vlnplot
Samples
updated 3 hours ago by
Bioinfotec
▴ 10 • written 6 hours ago by
starswillfade
▴ 10
0
votes
2
replies
138
views
why renaming Idents in Seurat object doesn't work?
Seurat
RenameIdents
R
updated 3 hours ago by
Bioinfotec
▴ 10 • written 11 hours ago by
Assa Yeroslaviz
★ 1.8k
0
votes
2
replies
86
views
BLAST using both nucleotides and taxonomic local databases
blast
ncbi
taxid
taxonomy
updated 1 hour ago by
GenoMax
141k • written 9 hours ago by
Begonia_pavonina
▴ 150
0
votes
2
replies
135
views
Highest variable features in single cell data
single-cell
updated 10 minutes ago by
Ram
43k • written 13 hours ago by
Kazo
• 0
0
votes
2
replies
141
views
Annovar using R package
Annovar
gnomAD
R
10 minutes ago by
DKA
▴ 40
0
votes
1
reply
77
views
Tutorial:
how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix
RNAseq
R
updated 4 minutes ago by
Ram
43k • written 17 hours ago by
Ming Tommy Tang
★ 3.9k
0
votes
1
reply
138
views
Network Alignment
plugin
Cytoscape
CytoMCS
updated 16 hours ago by
Scooter
▴ 280 • written 1 day ago by
Akash D
▴ 40
0
votes
1
reply
122
views
PCA plot
DESeq2
PCAplot
updated 6 hours ago by
jkim
▴ 170 • written 17 hours ago by
Aaliya
▴ 10
0
votes
1
reply
369
views
GAPIT p-value significance threshold
GAPIT
p-value
GWAS
updated 5 hours ago by
ginellegrenier
• 0 • written 4 months ago by
Clayton
• 0
0
votes
1
reply
28
views
Normalize scRNAseq data to housekeeping genes to compare several datasets
RNA-sequencing
housekeeping
Single-cell
normalization
updated 36 minutes ago by
ATpoint
82k • written 1 hour ago by
AaronJaime
• 0
0
votes
1
reply
106
views
Hide positions in alignment with 99% "–" characters to ignore single sequence insertions?
alignment
gaps
updated 13 hours ago by
b.contreras.moreira
▴ 170 • written 14 hours ago by
Broccoli
• 0
2
votes
1
reply
129
views
Finding orthologs between genome error
OMA
OMAbrowser
updated 11 hours ago by
Adrian Altenhoff
★ 1.1k • written 1 day ago by
hemantcnaik
• 0
1
vote
1
reply
85
views
ScRNAseq-How to correctly choose cell type marker genes
cellAssign
cell-markers
updated 10 minutes ago by
Ram
43k • written 6 hours ago by
Francesco
▴ 10
0
votes
0
replies
37
views
how to read graph_test output of monocle 3
monocle3
4 hours ago by
synat.keam
▴ 100
0
votes
0
replies
35
views
How to calculate correlation coefficient for chipseq?
chipseq
bigwigsummary
correlation
3 hours ago by
Emily
▴ 10
1
vote
0
replies
40
views
How to calculate reliable Ka/Ks or dN/dS ratio for genes of interest from VCF file
dnds
kaks
VCF
4 hours ago by
rohitsatyam102
▴ 850
0
votes
0
replies
91
views
News:
8th Berlin Summer School in NGS Data Analysis - Apply Now
DNA-seq
variant-calling
RNA-seq
illumina
transcriptomics
updated 10 minutes ago by
Ram
43k • written 1 day ago by
David Langenberger
11k
0
votes
0
replies
37
views
Is there a way to increase the automatic label text size in Cytoscape?
Cytoscape
3 hours ago by
avocado123
• 0
0
votes
0
replies
82
views
Can you give me an example of a small globular protein (PDB) that has disordered alpha-carbons?
protein
pdb
alpha-carbon
19 hours ago by
4fzcgueyp5
• 0
0
votes
0
replies
2
views
How to visualize/predict the final transcript from Delly output?
WGS
DELLY
just now by
simplitia
▴ 130
0
votes
0
replies
55
views
Why not use iBAQ for calculating differential abundance of proteins?
protein
maxquant
11 hours ago by
Aspire
▴ 300
0
votes
0
replies
34
views
News:
Master Meta-analysis with R (May 13-16) - Online!
Meta-Analysis
Statistics
R
updated 15 minutes ago by
Ram
43k • written 3 hours ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
48
views
Job:
CTO/founding engineer role at Voyant Bio
engineer
4 hours ago by
Assaf
• 0
43 results • Page
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Recent Votes
How to calculate reliable Ka/Ks or dN/dS ratio for genes of interest from VCF file
Detecting somatic variants in non-tumor tissue without normals
Answer: Sequence read length shorter than flow cell specification
Answer: Sequence read length shorter than flow cell specification
Comment: Why gatk VariantAnnotator required bam and coverage files
A: Generate Vcf.Gz File And Its Index File Vcf.Gz.Tbi
Visualization of ChIP-seq data using Heatmaps (Updated: 06/10/16)
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82k
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▴ 30
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Recent Replies
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix
by
Ram
43k
Thank you, the `csvtk spread` is super useful. I usually import into R using `lapply` then `Reduce` using `merge` but this might be easier.
Comment: Annovar using R package
by
DKA
▴ 40
Thank you for your guidance. The thing is that I am unfamiliar with using such environments, unfortunately.
Comment: Treatment VS Control in Single Cell RNAseq analysis
by
ATpoint
82k
Open a new question, with details.
Comment: Normalize scRNAseq data to housekeeping genes to compare several datasets
by
ATpoint
82k
I recommend https://bioconductor.org/books/3.18/OSCA.basic/normalization.html as well as the "advanced" section in this book.
Comment: Why gatk VariantAnnotator required bam and coverage files
by
QX
• 0
thank you!
Comment: Treatment VS Control in Single Cell RNAseq analysis
by
kilcdincer
▴ 10
Hello, I have more or less same experimental setting and was wondering how you proceeded with your analysis? Can I reach its GitHub reposit…
Comment: BLAST using both nucleotides and taxonomic local databases
by
GenoMax
141k
> I ask this as some BLAST command fields as scinames or sblastnames do not give any output with a classic nt BLAST If that information is…
Answer: BLAST using both nucleotides and taxonomic local databases
by
5heikki
11k
This has been discussed [many times][1] [1]: https://www.biostars.org/p/76551/
Answer: why renaming Idents in Seurat object doesn't work?
by
Bioinfotec
▴ 10
I think when you give indent to seuObj : Idents(seuObj) <- 'RNA_snn_res.0.1' You may wrongly assign other value to it such as …
Answer: ScRNAseq-How to correctly choose cell type marker genes
by
Bioinfotec
▴ 10
In fact, there is no gold standard for cell type annotation. To achieve correct cell type classification, you can combine the two methos. F…
Answer: ScRNA data question
by
Bioinfotec
▴ 10
In violin plot, a dot represents a cell. Actually, the straight lines you see in your infected image just means these cells have the same e…
Comment: Sequence read length shorter than flow cell specification
by
GenoMax
141k
> the have sent data with different sequencing read lengths: 55bp pair ended and 80bp single ended If they sent data that is not what you…
Comment: How to know synonymous and non-synonymous SNPs from transcriptome sequencing
by
rohitsatyam102
▴ 850
I have some off-the-chart dN/dS values for few genes (>20) when using your script on VCF obtained from a 20K plasmodium genomes (pf7K). | …
Answer: Sequence read length shorter than flow cell specification
by
ATpoint
82k
It is the amount of reagent in the kit that determines read length. Sometimes index cycle reagents are allocated to R1/R2 or they used anot…
Comment: Why gatk VariantAnnotator required bam and coverage files
by
Pierre Lindenbaum
161k
you don't need the bam file https://gatk.broadinstitute.org/hc/en-us/articles/13832654601755-VariantAnnotator : VariantAnnotator …
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