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537 results • Page
3 of 11
Sort: replies
Rank
Views
Votes
Replies
0
votes
3
replies
278
views
How do I handle it if there are multiple ENSEMBL IDs in one gene symbol in the scRNA sequencing data?
Seurat
scRNA-seq
count-matrix
17 days ago by
Jeyong
• 0
3
votes
3
replies
462
views
Free/open source 23andme-like analysis
SNPs
genomics
NGS
VCF
updated 5 days ago by
swbarnes2
14k • written 6 days ago by
joe
▴ 510
0
votes
3
replies
303
views
Help with mauve
mauve
updated 19 days ago by
Ram
43k • written 7 weeks ago by
reachedahead225
• 0
1
vote
3
replies
6.1k
views
Error for converting from gene symbol to Entrez IDs
Entrez-ID
org.Dr.eg.db
updated 8 days ago by
Ram
43k • written 5.5 years ago by
modarzi
▴ 170
2
votes
3
replies
3.0k
views
RNA-seq batch effect correction
RNA-Seq
batch-effect
sequencing
updated 6 days ago by
Ram
43k • written 6.9 years ago by
endikavarela
• 0
1
vote
3
replies
2.4k
views
Problem to remove subset of patients with plink
plink
PED
updated 2 days ago by
chrchang523
10k • written 6.1 years ago by
Ginevra
▴ 10
0
votes
3
replies
260
views
BLASTP web- <20aa peptides- interpreting results/ minimum E value?
blast
peptide
blastp
alignment
updated 13 days ago by
GenoMax
141k • written 13 days ago by
neish
• 0
1
vote
3
replies
344
views
Ensembl gene id conversion
biomart
ensembl
updated 9 days ago by
ATpoint
82k • written 11 days ago by
naveedhasan2000
• 0
0
votes
3
replies
611
views
Not all variants are annotated with AF - expected or a problem?
Variant-Calling
WGS
Alignment
updated 22 days ago by
Ram
43k • written 7 months ago by
Luiz
▴ 30
2
votes
3
replies
1.5k
views
Duplicate row name not allowed while reading the file in R
RNA-Seq
deseq2
Differential-Gene-expression
R
updated 15 days ago by
Ram
43k • written 4.9 years ago by
imanbh
• 0
1
vote
3
replies
349
views
how to do the repeatability filtering of vcf files?
snp
vcf.
updated 23 days ago by
Pierre Lindenbaum
161k • written 25 days ago by
Max
• 0
0
votes
3
replies
260
views
High number of detected genes per cell after doublet removal - scRNAseq data
scRNAseq
duoblet
28 days ago by
sarahmanderni
▴ 100
2
votes
3
replies
279
views
Extracting information from my VCF file
VCF
updated 29 days ago by
bioruffo
▴ 40 • written 29 days ago by
realtreeecat
• 0
1
vote
3
replies
1.7k
views
Using Nanoplot to asses quality of ONT data
ONT
Long-read-sequencing
NanoPlot
updated 19 days ago by
Ram
43k • written 2.3 years ago by
matt81rd
▴ 10
0
votes
3
replies
259
views
can't download and use mageck-vispr for R?
mageck-vispr
Rstudio
updated 23 days ago by
ATpoint
82k • written 23 days ago by
Vishal
• 0
0
votes
3
replies
1.8k
views
How to remove batch effect in copy number segment mean
Combat
CNA
Batch-Effect
updated 7 days ago by
Ram
43k • written 5.5 years ago by
sugus
▴ 150
1
vote
3
replies
193
views
Filter BAM to keep only alignments at an interval, ignoring reads spliced over
samtools
bam
splicing
2 days ago by
WouterDeCoster
47k
3
votes
3
replies
313
views
Volcano Plot Output Inquiry: Graphs Facing Down
rstudio
volcano-plot
25 days ago by
Pumla
• 0
0
votes
3
replies
701
views
PCR duplicates in FFPE RNASeq
PCR-duplicates
RNA-Seq
FFPE
Variant-Calling
updated 29 days ago by
Ram
43k • written 22 months ago by
Gama313
▴ 120
0
votes
3
replies
3.1k
views
Rna-seq for differential expression analysis
differential-expression
transcriptome
updated 6 days ago by
Ram
43k • written 9.0 years ago by
siddharth.patel.153
• 0
1
vote
3
replies
275
views
True variants selection
vcf
bcftools
updated 13 days ago by
dthorbur
★ 1.9k • written 14 days ago by
maevalefeuvre
• 0
2
votes
3
replies
928
views
Possible approach to select normal tissue samples for cancer RNA-Seq data without reference data for downstream analyses
R
RNA-Seq
DE
batch-effect
GTEx
updated 9 days ago by
Ram
43k • written 4.1 years ago by
svlachavas
▴ 790
1
vote
3
replies
387
views
multiple sequence alignment
BLAST
multiple-sequence-alignment
clustal-omega
MSA
updated 16 days ago by
Ram
43k • written 19 days ago by
catherinemaria2728
• 0
0
votes
3
replies
579
views
FindAllMarkers not working (Error (data layers are not joined. Please run JoinLayersWarning: When testing 1 versus all)
FindAllMarkers
seurat
re-clustering
27 days ago by
Nitin
• 0
1
vote
3
replies
253
views
CCA with random effects model
CCA
updated 23 days ago by
dariober
14k • written 23 days ago by
leranwangcs
▴ 120
1
vote
3
replies
4.1k
views
Evaluating removing batch effect tools with PCA or MDS?
bioconductor
limma
sva
r
batch-effect
updated 6 days ago by
Ram
43k • written 7.6 years ago by
Lluís R.
★ 1.2k
0
votes
3
replies
1.1k
views
Batch effect for SNP array
sva
combat
batch-effect
SNP
updated 9 days ago by
Ram
43k • written 4.2 years ago by
Taylor95
▴ 10
2
votes
3
replies
253
views
P-value Threshold Consideration in Multi-Sample RNA-Seq Experiment
statistics
RNA-Seq
p-value
updated 22 days ago by
Ram
43k • written 23 days ago by
Netanel
• 0
0
votes
3
replies
335
views
Resources regarding Proteomics (In-Silico)
molecular-simulation
docking
protein
proteomics
updated 23 days ago by
Ram
43k • written 5 weeks ago by
Saurabh
• 0
1
vote
3
replies
229
views
some error in building kraken2 database
metagenome
kraken2
1 day ago by
Art1ess
• 0
0
votes
3
replies
446
views
How do I get the gene annotations as a text file from a genbank file?
sequence-annotation
genbank
updated 26 days ago by
Ram
43k • written 27 days ago by
eae6d2e7
• 0
0
votes
3
replies
214
views
Peptide identification from Mass spec data
Transcriptomics
Proteins
Mass-spec
updated 20 days ago by
Ram
43k • written 21 days ago by
atharvakarkare14
▴ 10
2
votes
3
replies
1.1k
views
Polishing PACBIO corrected assembly using ONT and ILLUMINA data (.fastq)
fasta
Nanopore
long-read
fastq
updated 19 days ago by
Ram
43k • written 2.8 years ago by
K
▴ 10
0
votes
2
replies
365
views
How can I solve this error?
metal
7 days ago by
22211020193
• 0
1
vote
2
replies
269
views
Can I readmap short reads to rDNA references?
rDNA
assembly
updated 7 days ago by
Ram
43k • written 7 days ago by
aniigodwinn
• 0
0
votes
2
replies
263
views
RNAseq 1 control 2 different treatment
RNA-seq
9 days ago by
matteo.levorato
• 0
0
votes
2
replies
617
views
Seeking Alternative Tools for Predicting Mature microRNAs from Vertebrate Animal Precursors in In Silico Study
mirdeep2
maturebayes
microrna
updated 22 days ago by
Ram
43k • written 12 months ago by
Beatriz
• 0
0
votes
2
replies
264
views
trying to do some GSEA in python
python
GSEA
GO
updated 21 days ago by
Wayne
★ 2.0k • written 25 days ago by
aleksk779
• 0
0
votes
2
replies
210
views
Error with goodSamplesGenes()
R
WGCNA
28 days ago by
bioinfo_enthusiast
• 0
5
votes
2
replies
1.7k
views
Batch effects from sequencing samples accross multiple flow cells.
rna-seq
batch
batch-effect
sequencing
updated 8 days ago by
Ram
43k • written 2.9 years ago by
Mat
▴ 60
0
votes
2
replies
578
views
Bacterial contamination in human DNA sample
Long-read-sequencing
Bacterial-contamination
updated 19 days ago by
Ram
43k • written 22 months ago by
priya.bmg
▴ 60
0
votes
2
replies
192
views
Can't figure out plink --sample-diff
plink
14 days ago by
curious
▴ 750
0
votes
2
replies
265
views
WGCNA
PCA
WGCNA
EIGENGENE
13 days ago by
rajasekargutha
▴ 60
0
votes
2
replies
532
views
How to get the reference panel for UKBB
UKBB
GWAS
clump
6 days ago by
航太郎
• 0
1
vote
2
replies
921
views
vg surject for long reads
long-reads
vg
variation-graph
surject
updated 19 days ago by
Ram
43k • written 23 months ago by
ved_vyas
▴ 10
0
votes
2
replies
1.0k
views
proportional hazard assumption was not satisfied for a covariate
hazard-ratios
Cox-model
survival
updated 8 days ago by
Ram
43k • written 4.4 years ago by
akutasame
▴ 40
2
votes
2
replies
1.6k
views
read count for RNA sequencing via nanopore
long-reads
RNA-seq
gene-expression
read-count
updated 19 days ago by
Ram
43k • written 2.9 years ago by
gat
• 0
0
votes
2
replies
242
views
VCF annotation with gnomADv4 using R package
annotation
gnomADv4
R
VCF
7 days ago by
DKA
▴ 40
0
votes
2
replies
511
views
Gene expression assay Yeast sample prep
Live-cells
updated 22 days ago by
Ram
43k • written 22 months ago by
dshdixit
▴ 10
1
vote
2
replies
208
views
Flow Cytometry Data Analysis by Seurat
Seurat
updated 27 days ago by
Ram
43k • written 27 days ago by
gdfsnkfns
• 0
537 results • Page
3 of 11
Recent Votes
Answer: Figures are disappeared from html report of SnpEff
Comment: How to trim transcripts using information from NCBI contamination screen report
Filtering rRNA contamination (indicated by GC content plots) from RNA-seq data
Filtering rRNA contamination (indicated by GC content plots) from RNA-seq data
A: What is the VEP Impact column?
is oxford nanopore technology data paired or single end sequencing?
is oxford nanopore technology data paired or single end sequencing?
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Recent Replies
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
Comment: Adding CB tag to bam file
by
Pierre Lindenbaum
161k
samtools addreplacerg is for read groups. This is not what OP asked.
Comment: Adding CB tag to bam file
by
Maria
• 0
When I try ``` samtools addreplacerg -r "@CB\tID:$cell" -o $cell.bam $LINE``` the CB tag gets add to the header, but the tag in every line …
Answer: Figures are disappeared from html report of SnpEff
by
Pierre Lindenbaum
161k
the remote website providing the javascript or/and the images is down or you're now behind a proxy. Check the firefox console: https://fire…
Comment: Fetch table from clinvar database according to a list of rsid
by
Pierre Lindenbaum
161k
ah ! and your code doesn't work because clinvar ID is not a rs-ID.
Answer: Fetch table from clinvar database according to a list of rsid
by
Pierre Lindenbaum
161k
$ cat input.rs rs11203366 rs11203367 rs874881 rs776453694 rs80324279 rs324420 rs112766203 wget -…
Comment: Highest variable features in single cell data
by
ATpoint
82k
> and these cells are not even in a single cluster. What does this mean? If you run clustering on all cells then every cell is assigned t…
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