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 week
all time
today
this week
this month
this year
110 results • Page
1 of 3
Sort: replies
Rank
Views
Votes
Replies
0
votes
10
replies
346
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo
scRNA-seq
STAR
snRNA-seq
MGI
19 hours ago by
atowns21
• 0
2
votes
9
replies
781
views
TCGA2STAT Error: Firehose connection
FIREHOSE
TCGA
updated 21 hours ago by
LauferVA
4.2k • written 6 months ago by
Gnana
• 0
0
votes
8
replies
272
views
Error in cnetplot enrichplot package
R
updated 2 days ago by
Ram
43k • written 2 days ago by
Farhad
• 0
2
votes
7
replies
804
views
Removing duplicates
duplicates
ONT
minimap2
updated 5 days ago by
joe
▴ 510 • written 7 days ago by
quentinperriere
• 0
0
votes
6
replies
422
views
Use of Kraken output for functional analysis
metagenomics
kraken
shotgun
updated 13 hours ago by
gv
• 0 • written 23 days ago by
Srinka
▴ 20
1
vote
5
replies
236
views
Downsampling fastq file
downsample
fastq
updated 2 days ago by
Ram
43k • written 2 days ago by
marco.barr
▴ 80
0
votes
5
replies
5.9k
views
Calculate Radius of Gyration [python 3]
biopython
PDB
Radius of Gyration
python
protein
updated 4 days ago by
ndm1096
• 0 • written 6.5 years ago by
ac.research
▴ 30
2
votes
5
replies
673
views
what's the genomic location and name of gene responsible for orange and black patches in calico cats
genomes
updated 4 days ago by
Jesse
▴ 740 • written 5 days ago by
Ann
★ 2.4k
2
votes
5
replies
425
views
Marking duplicates using UMIs
Deduplication
UMI
updated 2 days ago by
i.sudbery
19k • written 3 days ago by
Lipika
• 0
0
votes
5
replies
257
views
Should I remove unlocalized scaffols in reference genome before alignment?
qualimap
alignment
minimap2
GRCh38
assembly
11 hours ago by
njornet
▴ 20
0
votes
4
replies
491
views
How to reduce the variation of CIBERSORTx results?
CIBERSORTx
deconcolution
6 days ago by
feather-W
• 0
0
votes
4
replies
572
views
Per base sequence content failed miserably
fastqc
sequence
trimmomatic
NGS
assembly
5 days ago by
Kai Xin
• 0
3
votes
4
replies
3.4k
views
any recommended tools for batch effect and normalization not written in R?
R
RNA-Seq
combat
python
batch-effect
updated 6 days ago by
Ram
43k • written 7.1 years ago by
dyollluap
▴ 310
2
votes
4
replies
236
views
interpretartion of a vcf file
calling
genotype
ONT
variant
diploid
14 hours ago by
samuelkalandarov2002
▴ 10
2
votes
4
replies
1.4k
views
How to fix Error in dat[, batch == batch_level] : (subscript) logical subscript too long when removing batch effects
microarray
combat
batch-effect
median-normalization
updated 6 days ago by
Ram
43k • written 18 months ago by
Dominique
• 0
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
224
views
some error in building kraken2 database
metagenome
kraken2
21 hours ago by
Art1ess
• 0
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
1
vote
3
replies
188
views
Filter BAM to keep only alignments at an interval, ignoring reads spliced over
samtools
bam
splicing
1 day ago by
WouterDeCoster
47k
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
3
votes
3
replies
461
views
Free/open source 23andme-like analysis
SNPs
genomics
NGS
VCF
updated 4 days ago by
swbarnes2
14k • written 5 days ago by
joe
▴ 510
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
0
votes
2
replies
2.8k
views
RNA-seq unbalanced batch effect correction
limma
RNA-Seq
edgeR
batch-effect
updated 6 days ago by
Ram
43k • written 7.0 years ago by
endikavarela
• 0
0
votes
2
replies
368
views
error in coding potential calculator CPC2
cpc
CPC2
coding-potential
5 days ago by
Ashok
• 0
0
votes
2
replies
530
views
How to get the reference panel for UKBB
UKBB
GWAS
clump
5 days ago by
航太郎
• 0
0
votes
2
replies
536
views
autodockvina
python
python3
autodock
updated 6 days ago by
Ram
43k • written 3 months ago by
iamsmor
• 0
0
votes
2
replies
310
views
GSEA analysis in R
GSEA
R
Arabidopsis
6 days ago by
Sudip
• 0
1
vote
2
replies
1.9k
views
Remove batch effect from exome data
NGS
exome-sequencing
batch-effect
updated 6 days ago by
Ram
43k • written 6.5 years ago by
Alternative
▴ 270
0
votes
2
replies
407
views
miRNAs quantification using mirdeep2 tool
differential-expression
mirdeep2
miRNA
5 days ago by
Ashok
• 0
0
votes
2
replies
131
views
different FeatureCounts output for the same data
fpkm
Counts
Rsubread
rna-seq
updated 3 hours ago by
Ram
43k • written 13 hours ago by
sehriban.buyukkilic
▴ 10
0
votes
2
replies
176
views
Low mapping rate with Salmon
RNA-seq
Salmon
Quantification
updated 2 days ago by
i.sudbery
19k • written 2 days ago by
Patadu94
• 0
0
votes
2
replies
190
views
How to calculate identity percentage between proteins contained in a FASTA file?
protein
FASTA
alignment
updated 3 hours ago by
Ram
43k • written 1 day ago by
v.berriosfarias
▴ 140
1
vote
2
replies
226
views
permutation test in edgeR
rna-seq
edgeR
updated 2 days ago by
Gordon Smyth
★ 7.0k • written 16 days ago by
Netanel
• 0
0
votes
2
replies
416
views
QC exclusion of A/T or G/C alleles to avoid strand issues
quality-control
SNV
QC
SNP
5 days ago by
_quantum_girl_
▴ 10
0
votes
2
replies
142
views
clustalo - align milions of short seq, memory issue
memory
clustalo
updated 2 days ago by
Mensur Dlakic
★ 27k • written 2 days ago by
emmanouil.a
▴ 120
0
votes
2
replies
251
views
bam merging for archaic samples
samtools
bam
updated 3 days ago by
Ram
43k • written 4 days ago by
Matteo Ungaro
▴ 100
0
votes
2
replies
365
views
How can I solve this error?
metal
6 days ago by
22211020193
• 0
0
votes
1
reply
398
views
How to add rowLinks, rowTree in SummarizedExperiment manually.
phylogenetic-tree
microbiome
updated 6 days ago by
Ram
43k • written 19 months ago by
Muhammad
• 0
0
votes
1
reply
184
views
Heatmap and rna-seq
RNA-Seq
Heatmap
and
updated 1 day ago by
Istvan Albert
100k • written 1 day ago by
qudrat.nii
▴ 10
0
votes
1
reply
107
views
How to solve this RoseTTAFold colaboratory error?
modeling
Google
Colaboratory
RoseTTAFold
protein
updated 18 hours ago by
Mensur Dlakic
★ 27k • written 1 day ago by
benguyarenbeyaz98
• 0
0
votes
1
reply
133
views
Plot DNA methylation level of DMR on the basis of certain genes
rrbs
methylkit
updated 1 day ago by
GenoMax
141k • written 1 day ago by
Srinka
▴ 20
1
vote
1
reply
150
views
Failed kmer content
kmer
illumina
ngs
updated 1 day ago by
Ram
43k • written 1 day ago by
Kasturi
• 0
0
votes
1
reply
132
views
Identification of Transgene insertion sites
Transgene
Whole-Genome-Sequencing
transgene-sites
updated 2 days ago by
Ram
43k • written 2 days ago by
Cameron.walker9900
• 0
0
votes
1
reply
816
views
Bulk RNAseq MACS Sort Quality Contamination
EdgeR
Batch-effect
RNA-Seq
updated 6 days ago by
Ram
43k • written 3.7 years ago by
jordan15
• 0
0
votes
1
reply
258
views
Downloading the raw microarray data from GEO
.gpr
microarray
.CEL
updated 5 days ago by
GenoMax
141k • written 5 days ago by
bioyas
▴ 10
0
votes
1
reply
1.8k
views
Advice required for remove batch effect which perfectly collinear with contrast of interest
RNA-seq
batch-effect
updated 6 days ago by
Ram
43k • written 6.6 years ago by
boymin2020
▴ 80
0
votes
1
reply
119
views
Subset Seurat object from Xenium spatial data
Seurat
Xenium
Spatial
updated 1 day ago by
bk11
★ 2.3k • written 1 day ago by
Susmita Mandal
▴ 110
1
vote
1
reply
388
views
Load a full GFF3 into annotation track using arrow (Apollo)
arrow
python-apollo
Apollo
5 days ago by
renan.igor
• 0
0
votes
1
reply
120
views
tbtool
tbtool
updated 2 days ago by
Ram
43k • written 2 days ago by
Raman
• 0
0
votes
1
reply
139
views
RNA-seq bacteria contamination
RNA-seq
updated 2 days ago by
GenoMax
141k • written 2 days ago by
sh
• 0
110 results • Page
1 of 3
Recent Votes
Comment: downloading genomes in fasta format from accession ids
Comment: PCA plot (Suggestions Needed)
Answer: PCA plot (Suggestions Needed)
PCA plot (Suggestions Needed)
Comment: To get p-values for the TPM
A: Where To Download Pam50 Gene Set?
A: Where To Download Pam50 Gene Set?
Recent Locations •
All
United States,
just now
United States,
1 minute ago
United States,
1 minute ago
Italy,
2 minutes ago
Canada,
4 minutes ago
Machhagan,
5 minutes ago
United States,
8 minutes ago
Recent Awards •
All
Popular Question
to
carlopecoraro2
★ 2.5k
Popular Question
to
daffodil
▴ 10
Popular Question
to
Russ
▴ 500
Popular Question
to
camillab.
▴ 160
Popular Question
to
pramach1
▴ 40
Popular Question
to
Adyasha
• 0
Popular Question
to
sehriban.buyukkilic
▴ 10
Recent Replies
Comment: Annovar using R package
by
Pierre Lindenbaum
161k
duplicate of your previous question: https://www.biostars.org/p/9592646/ why using R when there are shell-based tools like VEP ? slivar , …
Comment: Trouble with Pilon installation
by
Lissa Cruz Saavedra
• 0
Hi I am trying to install the software but I didn't find the way to clone from github. Could you help me with the pipeline of instruction…
Comment: Adding CB tag to bam file
by
swbarnes2
14k
I think both these programs are just adding the same tag to every line. I don't think either cares whether it's called RG or CB
Comment: PCA plot (Suggestions Needed)
by
swbarnes2
14k
Even if this was real data, the tiny numbers for the PC1 and PC2 indicate that the differences between the samples are all absolutely tiny.…
Comment: Creating Synthetic Sequences for a ML Model
by
biochugs
• 0
Thanks for the input. I'll continue to think of more ideas that may be achievable.
Comment: PCA plot (Suggestions Needed)
by
Jeremy
▴ 890
You could also try kernel PCA, which is a non-linear form of PCA, although this will be more time-consuming.
Comment: Troubleshooting RNA-seq data with DNA contamination
by
DKA
▴ 40
I have unstranded RNA-seq data. Please share the tool with me, if you do not mind.
Comment: PCA plot (Suggestions Needed)
by
Mensur Dlakic
★ 27k
Everything that @f1f58aed said, plus that there may be no data manipulation that will give you the clusters you expected. Sometimes there a…
Answer: Creating Synthetic Sequences for a ML Model
by
Mensur Dlakic
★ 27k
It is a good idea, though I don't see how it would work in practice. I think you will encounter at least one additional problem on top of …
Answer: PCA plot (Suggestions Needed)
by
Jeremy
▴ 890
Right now, the WT samples are clustering together, but you have one mutant sample off by itself, which could be an outlier. How did you sc…
Comment: Adding CB tag to bam file
by
GenoMax
141k
@yokofakun had written this: https://www.biostars.org/p/336965/ https://github.com/ruqianl/appendCB may also be useful.
Comment: Troubleshooting RNA-seq data with DNA contamination
by
GenoMax
141k
Please post information about your tool as a `tools` category post. Don't wait/ask other users to ask you.
Comment: Adding CB tag to bam file
by
Maria
• 0
Sorry for the delay in my answer, I got sidetracked. I am using ```samtools addreplacerg -r "@RG\tID:$cell" -o $cell.bam -h $LINE``` bu…
Answer: Troubleshooting RNA-seq data with DNA contamination
by
haibol2017
▴ 10
We just developed a R package to tackle this problem. Do you have stranded or unstranded RNA-seq data contaminated with gDNA? If you wou…
Comment: How to trim transcripts using information from NCBI contamination screen report
by
GenoMax
141k
`bbduk.sh` can use the transcripts as input. There is a `adapters.fa` included in the `resources` directory of the distribution. You can do…
Traffic: 2140 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