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41 results • Page
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76
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72
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19k
views
19 follow
Tutorial:
Clustering of DAVID gene enrichment results from gene expression studies
enrichment
david
12 hours ago by
Kevin Blighe
87k
14
votes
2
replies
7.0k
views
Trouble with Pilon installation
polishing
pilon
installation
updated 16 hours ago by
Lissa Cruz Saavedra
• 0 • written 7.3 years ago by
Rox
★ 1.4k
4
votes
7
replies
358
views
To get p-values for the TPM
P-value
TPM
RSEM
updated 5 hours ago by
dsull
★ 5.8k • written 1 day ago by
VITALA
• 0
3
votes
3
replies
2.3k
views
How to make a TSS enrichment plot in ATAC-seq analysis?
ATAC
updated just now by
sp
• 0 • written 22 months ago by
Dan
▴ 180
3
votes
13
replies
638
views
How to convert plink files to Hapmap Format
GWAS
Plink
updated 22 hours ago by
bk11
★ 2.3k • written 7 weeks ago by
Sofia
• 0
3
votes
8
replies
435
views
PCA plot (Suggestions Needed)
DESeq2
PCAplot
updated 9 hours ago by
swbarnes2
14k • written 1 day ago by
Aaliya
▴ 10
2
votes
1
reply
110
views
Finding orthologs between genome error
OMA
OMAbrowser
updated 4 hours ago by
Adrian Altenhoff
★ 1.1k • written 20 hours ago by
hemantcnaik
• 0
2
votes
4
replies
230
views
How to trim transcripts using information from NCBI contamination screen report
RNAseq
assembly
transcriptome
contamination
updated 21 hours ago by
GenoMax
141k • written 1 day ago by
Lada
▴ 30
2
votes
2
replies
62
views
Why gatk VariantAnnotator required bam and coverage files
gatk
VariantAnnotator
48 minutes ago by
QX
• 0
2
votes
3
replies
124
views
Figures are disappeared from html report of SnpEff
HTML
SnpEff
updated 3 hours ago by
Pierre Lindenbaum
161k • written 7 hours ago by
analyst
▴ 30
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 10 hours ago by
ZhangYuanfeng
• 0 • written 2.4 years ago by
Frazier Baker
• 0
2
votes
4
replies
172
views
Fetch table from clinvar database according to a list of rsid
clinvar
fetching
data
python
perl
5 hours ago by
ashaneev07
▴ 20
1
vote
1
reply
22
views
ScRNA data question
scRNA
Vlnplot
Samples
updated 6 minutes ago by
bk11
★ 2.3k • written 33 minutes ago by
starswillfade
▴ 10
1
vote
10
replies
868
views
Troubleshooting RNA-seq data with DNA contamination
RNA-seq
DESeq2
DNA-contamination
19 hours ago by
DKA
▴ 40
1
vote
2
replies
164
views
alignment result
RNA-seq
samtools
hisat2
8 hours ago by
ahmad.sajad4541
• 0
1
vote
8
replies
710
views
Adding CB tag to bam file
samtools
bam
updated 6 hours ago by
Pierre Lindenbaum
161k • written 6 days ago by
Maria
• 0
1
vote
0
replies
18
views
ScRNAseq-How to correctly choose cell type marker genes
cellAssign
cell
markers
41 minutes ago by
Francesco
▴ 10
0
votes
2
replies
572
views
Why cd-hit-est not work when sequence identity threshold<0.95?
genome
cluster
sequence
updated 11 hours ago by
Dateline
• 0 • written 21 months ago by
JZX
• 0
0
votes
0
replies
60
views
Tutorial:
how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix
RNAseq
R
11 hours ago by
Ming Tommy Tang
★ 3.9k
0
votes
0
replies
70
views
PCA plot
DESeq2
PCAplot
11 hours ago by
Aaliya
▴ 10
0
votes
1
reply
126
views
Annovar using R package
Annovar
gnomAD
R
updated 15 hours ago by
Pierre Lindenbaum
161k • written 18 hours ago by
DKA
▴ 40
0
votes
1
reply
126
views
Network Alignment
plugin
Cytoscape
CytoMCS
updated 10 hours ago by
Scooter
▴ 280 • written 1 day ago by
Akash D
▴ 40
0
votes
2
replies
153
views
Creating Synthetic Sequences for a ML Model
DNA
ML
updated 16 hours ago by
Mensur Dlakic
★ 27k • written 19 hours ago by
biochugs
• 0
0
votes
1
reply
115
views
GEMMA GWAS how to specify factor or numerical for covariates
covariate
GEMMA
GWAS
updated 22 hours ago by
Sofia
• 0 • written 1 day ago by
mawigoj318
• 0
0
votes
1
reply
92
views
Hide positions in alignment with 99% "–" characters to ignore single sequence insertions?
alignment
gaps
updated 7 hours ago by
b.contreras.moreira
▴ 170 • written 7 hours ago by
Broccoli
• 0
0
votes
2
replies
759
views
AGeNT LocatIt
AGeNT
LocatIt
WES
UMI
duplicates
updated 21 hours ago by
barslmn
★ 2.1k • written 2.8 years ago by
jhy
▴ 10
0
votes
4
replies
209
views
different FeatureCounts output for the same data
fpkm
Counts
Rsubread
rna-seq
5 hours ago by
sehriban.buyukkilic
▴ 10
0
votes
2
replies
220
views
How to calculate identity percentage between proteins contained in a FASTA file?
protein
FASTA
alignment
updated 19 hours ago by
Ram
43k • written 1 day ago by
v.berriosfarias
▴ 140
0
votes
0
replies
79
views
Is result interpretation of the modelHomotypic function of the DoubletFinder correct?
doublet
DoubletFinder
Seurat
modelHomotypic
updated 19 hours ago by
Ram
43k • written 1 day ago by
Jeyong
• 0
0
votes
0
replies
37
views
Why not use iBAQ for calculating differential abundance of proteins?
protein
maxquant
5 hours ago by
Aspire
▴ 300
0
votes
0
replies
86
views
News:
hands-on introduction to generalized linear models (GLMs) using R
Generalized-Linear-Models
GLM
R
updated 19 hours ago by
Ram
43k • written 1 day ago by
carlopecoraro2
★ 2.5k
0
votes
1
reply
81
views
why renaming Idents in Seurat object doesn't work?
Seurat
RenameIdents
R
4 hours ago by
Assa Yeroslaviz
★ 1.8k
0
votes
2
replies
112
views
Highest variable features in single cell data
cell
single
4 hours ago by
Kazo
• 0
0
votes
0
replies
88
views
Alternative splicing analysis using SUPPA tool - how to normalise counts?
rna-seq
single-cell
suppa
alternative-splicing
updated 19 hours ago by
Ram
43k • written 1 day ago by
newuser2024
• 0
0
votes
0
replies
32
views
BLAST using both nucleotides and taxonomic local databases
blast
ncbi
taxid
taxonomy
2 hours ago by
Begonia_pavonina
▴ 150
0
votes
0
replies
22
views
Calling SE and TE using ROSE
Calling
SE
2 hours ago by
Manhezz
• 0
0
votes
5
replies
223
views
Is it possible to get a list of representative genomes from a past RefSeq release?
representative
ncbi
asembly
refseq
updated 1 hour ago by
GenoMax
141k • written 1 day ago by
Bertalan_Takacs
▴ 90
0
votes
0
replies
96
views
One error problem occurred caused by data type during using GDCprepare to handle BRCA data
TCGA
GDCprepare
updated 19 hours ago by
Ram
43k • written 1 day ago by
glaciya2018
• 0
0
votes
4
replies
2.6k
views
Lositan freezing when generating selection table
LOSITAN
updated 12 hours ago by
evawillms183
• 0 • written 8.3 years ago by
andrepleao
• 0
0
votes
0
replies
72
views
Can you give me an example of a small globular protein (PDB) that has disordered alpha-carbons?
protein
pdb
alpha-carbon
13 hours ago by
4fzcgueyp5
• 0
0
votes
3
replies
250
views
Heatmap and rna-seq
RNA-Seq
Heatmap
and
updated 12 hours ago by
Kevin Blighe
87k • written 2 days ago by
qudrat.nii
▴ 10
41 results • Page
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Recent Votes
ScRNAseq-How to correctly choose cell type marker genes
ScRNA data question
Comment: SRA to BAM
Answer: What Is A "Spot" In Sra Format
Comment: Why gatk VariantAnnotator required bam and coverage files
Comment: Why gatk VariantAnnotator required bam and coverage files
discoSnp - reference-free finding of isolated SNPs from non assembled reads
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Comment: ScRNA data question
by
bk11
★ 2.3k
Which normalization method did you use for your data? I am guessing you had used SCTransform normalization for your data. Can you plot usin…
Comment: How to make a TSS enrichment plot in ATAC-seq analysis?
by
sp
• 0
Hi Dan, I was wondering if you found out how to make the same graph with NFR and NBR regions with different curves. I was able to recreate…
Comment: Why gatk VariantAnnotator required bam and coverage files
by
QX
• 0
I think the coverage could also computed from bam file itself, but let say I do not include the coverage, do you have any idea why it needs…
Comment: Is it possible to get a list of representative genomes from a past RefSeq releas
by
GenoMax
141k
I am moving my answer to a comment. At this point you should email NCBI help desk and ask them this question. If you get an answer then ple…
Comment: Figures are disappeared from html report of SnpEff
by
Pierre Lindenbaum
161k
the javascript in your html is deprecated or your firefox is just tool old.
Comment: Why gatk VariantAnnotator required bam and coverage files
by
Pierre Lindenbaum
161k
> I would like to ask why they may require the bam file for this function? hum.. if you want to add the coverage, where do you think gatk …
Comment: Figures are disappeared from html report of SnpEff
by
analyst
▴ 30
By following above approach I got this ![enter image description here][1] [1]: /media/images/b47490eb-d4c4-4f39-a7b2-f5b7b6b8
Comment: Highest variable features in single cell data
by
Kazo
• 0
I apologize for the confusion. What I meant to say is that, for example, the Trbv17 gene appears among the variable genes. However, when I …
Answer: why renaming Idents in Seurat object doesn't work?
by
Assa Yeroslaviz
★ 1.8k
I manage to find a workwround, but I don't understand what I did wrong here. my solution was to extract the cluster column as vector and…
Answer: Finding orthologs between genome error
by
Adrian Altenhoff
★ 1.1k
Hi, thanks for letting us know. In a recent software update, we introduced a problem with the written splice information in the cached …
Comment: Fetch table from clinvar database according to a list of rsid
by
ashaneev07
▴ 20
so which one should i prefer? i don't need the entire results i need the condition-Germline table only. (for eg:-from, https://www.ncbi.nlm…
Comment: To get p-values for the TPM
by
dsull
★ 5.8k
OK, not sure why your intention is to use RSEM p-values for, but at least tell us the commands you ran then otherwise how are we supposed t…
Comment: Fetch table from clinvar database according to a list of rsid
by
Pierre Lindenbaum
161k
> Don't forget to follow up on your threads. If an answer was helpful, you should upvote it; if the answer resolved your question, you shou…
Comment: different FeatureCounts output for the same data
by
sehriban.buyukkilic
▴ 10
Sure, I'll inquire about the version of Rsubread. I'll keep you posted if it works :) Thanks
Comment: different FeatureCounts output for the same data
by
sehriban.buyukkilic
▴ 10
Yeah, let me show you my featureCounts result, it looks like this. It's too low. [1]: /media/images/eb8293fe-e6ae-4b02-92e2-0ba2075b
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