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527 results • Page
3 of 11
Sort: replies
Rank
Views
Votes
Replies
3
votes
3
replies
469
views
Free/open source 23andme-like analysis
SNPs
genomics
NGS
VCF
updated 5 days ago by
swbarnes2
14k • written 7 days ago by
joe
▴ 510
3
votes
3
replies
316
views
Volcano Plot Output Inquiry: Graphs Facing Down
rstudio
volcano-plot
26 days ago by
Pumla
• 0
1
vote
3
replies
254
views
CCA with random effects model
CCA
updated 23 days ago by
dariober
14k • written 24 days ago by
leranwangcs
▴ 120
2
votes
3
replies
3.0k
views
RNA-seq batch effect correction
RNA-Seq
batch-effect
sequencing
updated 7 days ago by
Ram
43k • written 7.0 years ago by
endikavarela
• 0
0
votes
3
replies
583
views
FindAllMarkers not working (Error (data layers are not joined. Please run JoinLayersWarning: When testing 1 versus all)
FindAllMarkers
seurat
re-clustering
28 days ago by
Nitin
• 0
0
votes
3
replies
265
views
rRNA depletion of RIP-seq samples
rRNA
RIP-seq
updated 16 days ago by
joe
▴ 510 • written 16 days ago by
CrisRisu
• 0
1
vote
3
replies
204
views
Filter BAM to keep only alignments at an interval, ignoring reads spliced over
samtools
bam
splicing
2 days ago by
WouterDeCoster
47k
0
votes
3
replies
613
views
Not all variants are annotated with AF - expected or a problem?
Variant-Calling
WGS
Alignment
updated 23 days ago by
Ram
43k • written 7 months ago by
Luiz
▴ 30
0
votes
3
replies
261
views
BLASTP web- <20aa peptides- interpreting results/ minimum E value?
blast
peptide
blastp
alignment
updated 14 days ago by
GenoMax
141k • written 14 days ago by
neish
• 0
1
vote
3
replies
350
views
how to do the repeatability filtering of vcf files?
snp
vcf.
updated 24 days ago by
Pierre Lindenbaum
161k • written 25 days ago by
Max
• 0
1
vote
3
replies
4.1k
views
Evaluating removing batch effect tools with PCA or MDS?
bioconductor
limma
sva
r
batch-effect
updated 7 days ago by
Ram
43k • written 7.6 years ago by
Lluís R.
★ 1.2k
0
votes
3
replies
261
views
can't download and use mageck-vispr for R?
mageck-vispr
Rstudio
updated 23 days ago by
ATpoint
82k • written 24 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 8 days ago by
Ram
43k • written 5.5 years ago by
sugus
▴ 150
0
votes
3
replies
260
views
High number of detected genes per cell after doublet removal - scRNAseq data
scRNAseq
duoblet
29 days ago by
sarahmanderni
▴ 100
0
votes
3
replies
317
views
10x GEX and ADT data analysis in Seurat
Seurat
scRNA-seq
ADT
Cite-seq
GEX
updated 12 days ago by
ATpoint
82k • written 14 days ago by
gdfsnkfns
• 0
1
vote
3
replies
2.5k
views
Problem to remove subset of patients with plink
plink
PED
updated 3 days ago by
chrchang523
10k • written 6.1 years ago by
Ginevra
▴ 10
1
vote
3
replies
389
views
multiple sequence alignment
BLAST
multiple-sequence-alignment
clustal-omega
MSA
updated 17 days ago by
Ram
43k • written 20 days ago by
catherinemaria2728
• 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 10 days ago by
Ram
43k • written 4.1 years ago by
svlachavas
▴ 790
0
votes
3
replies
216
views
Peptide identification from Mass spec data
Transcriptomics
Proteins
Mass-spec
updated 21 days ago by
Ram
43k • written 21 days ago by
atharvakarkare14
▴ 10
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 27 days ago by
Ram
43k • written 27 days ago by
eae6d2e7
• 0
2
votes
3
replies
1.1k
views
Polishing PACBIO corrected assembly using ONT and ILLUMINA data (.fastq)
fasta
Nanopore
long-read
fastq
updated 20 days ago by
Ram
43k • written 2.8 years ago by
K
▴ 10
0
votes
3
replies
279
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
18 days ago by
Jeyong
• 0
1
vote
3
replies
276
views
True variants selection
vcf
bcftools
updated 13 days ago by
dthorbur
★ 1.9k • written 14 days ago by
maevalefeuvre
• 0
0
votes
3
replies
3.1k
views
Rna-seq for differential expression analysis
differential-expression
transcriptome
updated 7 days ago by
Ram
43k • written 9.0 years ago by
siddharth.patel.153
• 0
2
votes
3
replies
254
views
P-value Threshold Consideration in Multi-Sample RNA-Seq Experiment
statistics
RNA-Seq
p-value
updated 23 days ago by
Ram
43k • written 23 days ago by
Netanel
• 0
1
vote
3
replies
6.1k
views
Error for converting from gene symbol to Entrez IDs
Entrez-ID
org.Dr.eg.db
updated 9 days ago by
Ram
43k • written 5.5 years ago by
modarzi
▴ 170
0
votes
3
replies
1.1k
views
Batch effect for SNP array
sva
combat
batch-effect
SNP
updated 10 days ago by
Ram
43k • written 4.2 years ago by
Taylor95
▴ 10
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 16 days ago by
Ram
43k • written 4.9 years ago by
imanbh
• 0
0
votes
3
replies
305
views
Help with mauve
mauve
updated 20 days ago by
Ram
43k • written 7 weeks ago by
reachedahead225
• 0
0
votes
3
replies
337
views
Resources regarding Proteomics (In-Silico)
molecular-simulation
docking
protein
proteomics
updated 24 days ago by
Ram
43k • written 5 weeks ago by
Saurabh
• 0
0
votes
2
replies
1.0k
views
proportional hazard assumption was not satisfied for a covariate
hazard-ratios
Cox-model
survival
updated 9 days ago by
Ram
43k • written 4.4 years ago by
akutasame
▴ 40
0
votes
2
replies
266
views
WGCNA
PCA
WGCNA
EIGENGENE
14 days ago by
rajasekargutha
▴ 60
0
votes
2
replies
316
views
Help with understanding the identifier mapping tables in the backend of HUMAnN
metagenomics
metacyc
enzyme
biobakery
humann
12 days ago by
O.rka
▴ 710
2
votes
2
replies
266
views
A pipeline for prediction and annotation of obelisks
rna-seq
updated 29 days ago by
Pierre Lindenbaum
161k • written 4 weeks ago by
fred.s.kremer
▴ 110
2
votes
2
replies
1.6k
views
read count for RNA sequencing via nanopore
long-reads
RNA-seq
gene-expression
read-count
updated 20 days ago by
Ram
43k • written 2.9 years ago by
gat
• 0
1
vote
2
replies
922
views
vg surject for long reads
long-reads
vg
variation-graph
surject
updated 20 days ago by
Ram
43k • written 23 months ago by
ved_vyas
▴ 10
1
vote
2
replies
1.7k
views
Batch effects and MDSPlot in limma
limma
Batch-effect
MDS
Galaxy
updated 9 days ago by
Ram
43k • written 4.8 years ago by
sonayuv
• 0
0
votes
2
replies
534
views
How to get the reference panel for UKBB
UKBB
GWAS
clump
7 days ago by
航太郎
• 0
0
votes
2
replies
410
views
miRNAs quantification using mirdeep2 tool
differential-expression
mirdeep2
miRNA
7 days ago by
Ashok
• 0
1
vote
2
replies
267
views
Can I compare kallisto counts from samples with different amount of reads?
RNA-seq
kallisto
9 days ago by
bioinfo
▴ 150
0
votes
2
replies
209
views
novel and know mir156 and mir172
a
updated 29 days ago by
gayachit
▴ 200 • written 29 days ago by
Fadmo
• 0
0
votes
2
replies
246
views
VCF annotation with gnomADv4 using R package
annotation
gnomADv4
R
VCF
8 days ago by
DKA
▴ 40
0
votes
2
replies
56
views
Create a new bed file with all pairwise combinations between two other bed files, based on bp distance
SNPs
BED
eqtl
bedtools
44 minutes ago by
J
• 0
0
votes
2
replies
314
views
Adding Clinvar data source to funcotator
gatk
Clinvar
funcotator
gnomad
updated 25 days ago by
Pierre Lindenbaum
161k • written 25 days ago by
Mojtaba
• 0
0
votes
2
replies
368
views
How can I solve this error?
metal
8 days ago by
22211020193
• 0
0
votes
2
replies
282
views
Are GeneExpression Subtype annotations removed from TCGA-GBM?
tcga-gbm
subtyping
tcga
updated 13 days ago by
Zhenyu Zhang
★ 1.2k • written 13 days ago by
Apollonia
• 0
0
votes
2
replies
192
views
Low mapping rate with Salmon
RNA-seq
Salmon
Quantification
updated 3 days ago by
i.sudbery
19k • written 3 days ago by
Patadu94
• 0
1
vote
2
replies
821
views
Replacing default numbers with geneNames in enhancedVolcano
EnhancedVolcano
updated 23 days ago by
Ram
43k • written 2.6 years ago by
Mohan
• 0
0
votes
2
replies
194
views
Can't figure out plink --sample-diff
plink
15 days ago by
curious
▴ 750
0
votes
2
replies
210
views
Error with goodSamplesGenes()
R
WGCNA
29 days ago by
bioinfo_enthusiast
• 0
527 results • Page
3 of 11
Recent Votes
Answer: Seurat merge and batch correction
Comment: How to convert plink files to Hapmap Format
Comment: How to convert plink files to Hapmap Format
Comment: How to convert plink files to Hapmap Format
Comment: How to convert plink files to Hapmap Format
Comment: How to convert plink files to Hapmap Format
Answer: Missing protein (VEGF-A) in String db
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Recent Replies
Comment: Create a new bed file with all pairwise combinations between two other bed files
by
J
• 0
Thank you for replying Pierre. I first added a third column to the SNP bed file, so that I would get a range of 1 for each SNP awk 'B…
Comment: Create a new bed file with all pairwise combinations between two other bed files
by
Pierre Lindenbaum
161k
> using bcftools Show us what you tried
Answer: gvcf joint calling
by
Jeremy Leipzig
22k
> Hi, guys, there is a question about the genomic gVCF file. I wonder > that since gVCF contains the non-var block records, why after merge…
Comment: Missing protein (VEGF-A) in String db
by
shalespringer
• 0
Thank you for replying here; this helped me figure out why MAPK10 was missing from my results. It was also marked as a pseudogene in the En…
Comment: How to convert plink files to Hapmap Format
by
Sofia
• 0
These are the first lines of the output: (Please is it normal to have NA in the P value column ?) CHR …
Comment: How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq librarie
by
atowns21
• 0
So I used the barcodes that I created (combos of positions 1-10 and 11-20) and I obtained similar alignment stats as the paper I pulled the…
Comment: How to convert plink files to Hapmap Format
by
Sofia
• 0
Thank you so much, it actually worked!
Answer: Rare Disease Variant Pathway Analysis
by
LauferVA
4.2k
Hi @efc1e545 , First a caveat. the information we most need in order to help guide you to a successful conclusion is not provided in thi…
Answer: Sequence read length shorter than flow cell specification
by
swbarnes2
14k
The company probably had you share your run with someone who needed the extra bases. So you get the extra bases free. Just use them unle…
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…
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