Latest
Open
Jobs
Tutorials
Tags
About
FAQ
Community
Planet
New Post
Log In
New Post
Latest
Open
News
Jobs
Tutorials
Forum
Tags
Planet
Users
Log In
Sign Up
About
Limit : this month
all time
today
this week
this month
this year
515 results • Page
3 of 11
Sort: replies
Rank
Views
Votes
Replies
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
0
votes
3
replies
1.8k
views
How to remove batch effect in copy number segment mean
Combat
CNA
Batch-Effect
updated 9 days ago by
Ram
43k • written 5.5 years ago by
sugus
▴ 150
1
vote
3
replies
212
views
Filter BAM to keep only alignments at an interval, ignoring reads spliced over
samtools
bam
splicing
3 days ago by
WouterDeCoster
47k
3
votes
3
replies
470
views
Free/open source 23andme-like analysis
SNPs
genomics
NGS
VCF
updated 6 days ago by
swbarnes2
14k • written 7 days ago by
joe
▴ 510
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
2
votes
3
replies
1.1k
views
Polishing PACBIO corrected assembly using ONT and ILLUMINA data (.fastq)
fasta
Nanopore
long-read
fastq
updated 21 days ago by
Ram
43k • written 2.9 years ago by
K
▴ 10
1
vote
3
replies
348
views
Ensembl gene id conversion
biomart
ensembl
updated 10 days ago by
ATpoint
82k • written 12 days ago by
naveedhasan2000
• 0
0
votes
3
replies
1.1k
views
Batch effect for SNP array
sva
combat
batch-effect
SNP
updated 11 days ago by
Ram
43k • written 4.2 years ago by
Taylor95
▴ 10
3
votes
3
replies
317
views
Volcano Plot Output Inquiry: Graphs Facing Down
rstudio
volcano-plot
27 days ago by
Pumla
• 0
2
votes
3
replies
3.0k
views
RNA-seq batch effect correction
RNA-Seq
batch-effect
sequencing
updated 8 days ago by
Ram
43k • written 7.0 years ago by
endikavarela
• 0
1
vote
3
replies
2.5k
views
Problem to remove subset of patients with plink
plink
PED
updated 4 days ago by
chrchang523
10k • written 6.1 years ago by
Ginevra
▴ 10
0
votes
3
replies
320
views
10x GEX and ADT data analysis in Seurat
Seurat
scRNA-seq
ADT
Cite-seq
GEX
updated 13 days ago by
ATpoint
82k • written 15 days ago by
gdfsnkfns
• 0
0
votes
3
replies
614
views
Not all variants are annotated with AF - expected or a problem?
Variant-Calling
WGS
Alignment
updated 24 days ago by
Ram
43k • written 7 months ago by
Luiz
▴ 30
0
votes
3
replies
307
views
Help with mauve
mauve
updated 21 days ago by
Ram
43k • written 7 weeks ago by
reachedahead225
• 0
0
votes
3
replies
199
views
Highest variable features in single cell data
single-cell
updated 2 hours ago by
bk11
★ 2.4k • written 1 day ago by
Kazo
• 0
1
vote
3
replies
351
views
how to do the repeatability filtering of vcf files?
snp
vcf.
updated 25 days ago by
Pierre Lindenbaum
161k • written 26 days ago by
Max
• 0
0
votes
3
replies
266
views
rRNA depletion of RIP-seq samples
rRNA
RIP-seq
updated 17 days ago by
joe
▴ 510 • written 17 days ago by
CrisRisu
• 0
0
votes
3
replies
263
views
BLASTP web- <20aa peptides- interpreting results/ minimum E value?
blast
peptide
blastp
alignment
updated 15 days ago by
GenoMax
141k • written 15 days ago by
neish
• 0
0
votes
3
replies
261
views
can't download and use mageck-vispr for R?
mageck-vispr
Rstudio
updated 24 days ago by
ATpoint
82k • written 25 days ago by
Vishal
• 0
1
vote
3
replies
276
views
True variants selection
vcf
bcftools
updated 14 days ago by
dthorbur
★ 1.9k • written 15 days ago by
maevalefeuvre
• 0
1
vote
3
replies
4.1k
views
Evaluating removing batch effect tools with PCA or MDS?
bioconductor
limma
sva
r
batch-effect
updated 8 days ago by
Ram
43k • written 7.6 years ago by
Lluís R.
★ 1.2k
1
vote
3
replies
250
views
some error in building kraken2 database
metagenome
kraken2
2 days ago by
Art1ess
• 0
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 17 days ago by
Ram
43k • written 4.9 years ago by
imanbh
• 0
0
votes
3
replies
585
views
FindAllMarkers not working (Error (data layers are not joined. Please run JoinLayersWarning: When testing 1 versus all)
FindAllMarkers
seurat
re-clustering
29 days ago by
Nitin
• 0
1
vote
3
replies
1.7k
views
Using Nanoplot to asses quality of ONT data
ONT
Long-read-sequencing
NanoPlot
updated 21 days ago by
Ram
43k • written 2.3 years ago by
matt81rd
▴ 10
0
votes
3
replies
447
views
How do I get the gene annotations as a text file from a genbank file?
sequence-annotation
genbank
updated 28 days ago by
Ram
43k • written 28 days ago by
eae6d2e7
• 0
1
vote
3
replies
390
views
multiple sequence alignment
BLAST
multiple-sequence-alignment
clustal-omega
MSA
updated 18 days ago by
Ram
43k • written 21 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 11 days ago by
Ram
43k • written 4.1 years ago by
svlachavas
▴ 790
0
votes
3
replies
338
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
3
replies
218
views
Peptide identification from Mass spec data
Transcriptomics
Proteins
Mass-spec
updated 22 days ago by
Ram
43k • written 22 days ago by
atharvakarkare14
▴ 10
1
vote
3
replies
255
views
CCA with random effects model
CCA
updated 24 days ago by
dariober
14k • written 25 days ago by
leranwangcs
▴ 120
1
vote
2
replies
327
views
BAM to CRAM and BAM recover with smaller size
BAM
samtools
CRAM
updated 23 days ago by
jkbonfield
★ 1.2k • written 6 weeks ago by
geocarvalho
▴ 360
0
votes
2
replies
266
views
Regions not clear in VCF
whole-exome
variant-calling
updated 18 days ago by
Ram
43k • written 19 days ago by
priya.bmg
▴ 60
0
votes
2
replies
513
views
Gene expression assay Yeast sample prep
Live-cells
updated 24 days ago by
Ram
43k • written 22 months ago by
dshdixit
▴ 10
1
vote
2
replies
274
views
Can I readmap short reads to rDNA references?
rDNA
assembly
updated 9 days ago by
Ram
43k • written 9 days ago by
aniigodwinn
• 0
0
votes
2
replies
258
views
Statistical Advice Needed for RNAseq Data Analysis
Statistical-Significance
Genomics
RNA-seq
Data-Analysis
updated 10 days ago by
Ram
43k • written 11 days ago by
David
• 0
5
votes
2
replies
1.7k
views
Batch effects from sequencing samples accross multiple flow cells.
rna-seq
batch
batch-effect
sequencing
updated 10 days ago by
Ram
43k • written 2.9 years ago by
Mat
▴ 60
0
votes
2
replies
317
views
GSEA analysis in R
GSEA
R
Arabidopsis
8 days ago by
Sudip
• 0
0
votes
2
replies
266
views
WGCNA
PCA
WGCNA
EIGENGENE
14 days ago by
rajasekargutha
▴ 60
0
votes
2
replies
247
views
VCF annotation with gnomADv4 using R package
annotation
gnomADv4
R
VCF
9 days ago by
DKA
▴ 40
1
vote
2
replies
923
views
vg surject for long reads
long-reads
vg
variation-graph
surject
updated 21 days ago by
Ram
43k • written 23 months ago by
ved_vyas
▴ 10
0
votes
2
replies
410
views
miRNAs quantification using mirdeep2 tool
differential-expression
mirdeep2
miRNA
7 days ago by
Ashok
• 0
0
votes
2
replies
210
views
novel and know mir156 and mir172
a
updated 29 days ago by
gayachit
▴ 200 • written 4 weeks ago by
Fadmo
• 0
1
vote
2
replies
267
views
Can I compare kallisto counts from samples with different amount of reads?
RNA-seq
kallisto
10 days ago by
bioinfo
▴ 150
0
votes
2
replies
316
views
Help with understanding the identifier mapping tables in the backend of HUMAnN
metagenomics
metacyc
enzyme
biobakery
humann
13 days ago by
O.rka
▴ 710
1
vote
2
replies
1.7k
views
Batch effects and MDSPlot in limma
limma
Batch-effect
MDS
Galaxy
updated 10 days ago by
Ram
43k • written 4.8 years ago by
sonayuv
• 0
1
vote
2
replies
821
views
Replacing default numbers with geneNames in enhancedVolcano
EnhancedVolcano
updated 24 days ago by
Ram
43k • written 2.6 years ago by
Mohan
• 0
2
votes
2
replies
1.6k
views
read count for RNA sequencing via nanopore
long-reads
RNA-seq
gene-expression
read-count
updated 21 days ago by
Ram
43k • written 2.9 years ago by
gat
• 0
0
votes
2
replies
196
views
Can't figure out plink --sample-diff
plink
16 days ago by
curious
▴ 750
0
votes
2
replies
315
views
Adding Clinvar data source to funcotator
gatk
Clinvar
funcotator
gnomad
updated 26 days ago by
Pierre Lindenbaum
161k • written 26 days ago by
Mojtaba
• 0
515 results • Page
3 of 11
Recent Votes
Comment: Create a new bed file with all pairwise combinations between two other bed files
Answer: Create a new bed file with all pairwise combinations between two other bed files
Answer: Create a new bed file with all pairwise combinations between two other bed files
Answer: Create a new bed file with all pairwise combinations between two other bed files
Answer: Trimming tools - your experience please?
Answer: Trimming tools - your experience please?
Answer: Trimming tools - your experience please?
Recent Locations •
All
France/Nantes/Institut du Thorax - INSERM UMR1087,
just now
Mt. Pleasant, MI,
just now
United States,
2 minutes ago
United States,
5 minutes ago
United States,
5 minutes ago
Nigeria,
5 minutes ago
Palau,
10 minutes ago
Recent Awards •
All
Scholar
to
Alex Reynolds
35k
Popular Question
to
chaco001
▴ 40
Commentator
to
GenoMax
141k
Popular Question
to
rheab1230
▴ 140
Popular Question
to
BioinfGuru
★ 1.7k
Scholar
to
bk11
★ 2.4k
Popular Question
to
vinayjrao
▴ 250
Recent Replies
Answer: How to use limma to find differentially expressed genes in response to a continu
by
Gordon Smyth
★ 7.0k
There's no need for form a contrast because the score variable is already in the model. A continuous variable is its own contrast. Just run…
Comment: Create a new bed file with all pairwise combinations between two other bed files
by
J
▴ 10
Oh wow, bedops closest-features, how did I overlook that!! I didn't know about it; thank you! Your awk script is beautiful. This worked per…
Comment: Create a new bed file with all pairwise combinations between two other bed files
by
J
▴ 10
Thank you Pierre! I'll try this out with my full data set.
Answer: DNA methylation preprocessing
by
cao510927
▴ 30
I happend to see one paper doing the similar thing, share it with you guys, "A systematic evaluation of normalization methods and probe rep…
Answer: Create a new bed file with all pairwise combinations between two other bed files
by
Alex Reynolds
35k
I think Pierre's answer might be correct for your test input, but it doesn't account for the start position of the reference element and so…
Comment: Highest variable features in single cell data
by
bk11
★ 2.4k
You need to be clear about how `Seurat` defines highly variable genes here. Highly variable genes are the genes that have very high express…
Comment: Heatmap and rna-seq
by
GenoMax
141k
Please include a link when you are recommending a tool. There can be programs with similar names.
Answer: Heatmap and rna-seq
by
dsull
★ 5.8k
Check out clustergrammer from Avi Ma'ayan's lab.
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix
by
Ram
43k
Simple: ```r data <- lapply(files, read_tsv) data <- Reduce(merge, data) # or Reduce(full_join, data) ``` <a href="" title="Text added bec…
Answer: Source other conda environments in a nextflow pipeline when nextflow itself is i
by
ATpoint
82k
You can make each process use a dedicated environment, see https://www.nextflow.io/docs/latest/conda.html#use-existing-conda-environments …
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix
by
BioinfGuru
★ 1.7k
Hi, Just thought I'd share this code snippet here for when each file contains multiple samples. I tried using lapply (as suggested by Ram)…
Comment: Low mapping rate with Salmon
by
i.sudbery
19k
Take your STAR alignment and sum all the counts for each gene. You can either do this by providing an annotation to STAR, or by running fea…
Comment: How to convert plink files to Hapmap Format
by
bk11
★ 2.4k
If you run your data with plink 2.0, you will have ERRCODE column in your result file showing the reason behind "NA" p-value. https://www.b…
Comment: genome assembly records not present in assembly_summary.txt
by
sapuizait
▴ 10
jesus its in the Genbank file and I was looking at the refseq! I m such a moron - thanks for pointing it out -sorry about that :(
Comment: ScRNA data question
by
bk11
★ 2.4k
I wonder how the `Vlnplots` will look if you normalize the data using `NormalizeData()` function in `Seurat`. The flat line in your plot ar…
Traffic: 2230 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6