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753 results • Page
3 of 16
Sort: Votes
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Views
Votes
Replies
3
votes
2
replies
285
views
imputation through beagle
panel
beagle
reference
imputation
4 days ago by
analyst
▴ 50
3
votes
3
replies
368
views
Is it possible to bulk download files from GEO repository?
RNA-seq
Galaxy
Tanscriptomics
updated 18 days ago by
noodle
▴ 580 • written 19 days ago by
WUSCHEL
▴ 760
3
votes
0
replies
241
views
News:
Webinar “Learning Single-cell Atlases” with Dr. Fabian Theis, author of Scanpy on May 8
Scanpy
Generative-AI
scRNA
Machine-Learning
updated 21 days ago by
Ram
43k • written 21 days ago by
Claire Watson
▴ 60
3
votes
8
replies
690
views
Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA2 - where to go from here?
nf-core
16S
amplicon
dada2
ampliseq
updated 11 days ago by
Chris Dean
▴ 410 • written 15 days ago by
sovrappensiero
▴ 100
3
votes
3
replies
3.0k
views
Quick way to Identify batch effect from covariates?
bioconductor
batch-effect
updated 29 days ago by
Ram
43k • written 7.9 years ago by
James Ashmore
★ 3.4k
3
votes
8
replies
4.2k
views
Using FPKM and TPM values for batch correction for Single Cell RNA-Seq
fpkm
scRNA-seq
RNA-Seq
tpm
batch-effect
updated 29 days ago by
Ram
43k • written 4.6 years ago by
hkarakurt
▴ 180
3
votes
4
replies
364
views
finding evidence(s) of a peptide translated from an "Upstream Open Reading Frame (uORF)"
UTR
masspec
uORF
peptide
updated 1 day ago by
GenoMax
142k • written 1 day ago by
Pierre Lindenbaum
161k
3
votes
3
replies
269
views
Gene Specific coverage from WGS data
WGS
SARS-CoV2
updated 4 days ago by
Ram
43k • written 18 days ago by
Adyasha
• 0
3
votes
2
replies
381
views
what is the purpose of indexing the reference genome (Kallisto)
indexing
Kallisto
updated 21 days ago by
dsull
★ 6.0k • written 22 days ago by
Aaliya
▴ 10
3
votes
0
replies
1.1k
views
Tool:
Sars-Cov-2 Genome & ACE 2 Exploration
sequence
alignment
SNP
genome
12 days ago by
Ibrahim Tanyalcin
★ 1.2k
3
votes
3
replies
552
views
Free/open source 23andme-like analysis
SNPs
genomics
NGS
VCF
updated 28 days ago by
swbarnes2
14k • written 29 days ago by
noodle
▴ 580
3
votes
6
replies
2.0k
views
7 follow
DNA methylation preprocessing
SWAN
DNA
methylation
Funnorm
updated 21 days ago by
Ram
43k • written 2.4 years ago by
SYOSY
▴ 10
3
votes
2
replies
193
views
Publish a Letter in higher impact vs Research article in lower impact
Article
Letter
Journal
updated 4 days ago by
ATpoint
82k • written 5 days ago by
jennyp0706
• 0
3
votes
3
replies
371
views
Sequence read length shorter than flow cell specification
illumina
NGS
sequencing
updated 22 days ago by
swbarnes2
14k • written 22 days ago by
M
• 0
3
votes
1
reply
282
views
Seurat merge and batch correction
Seurat
updated 24 days ago by
Ram
43k • written 25 days ago by
sooni
▴ 20
3
votes
6
replies
491
views
install package: package ‘gmwm’ is not available for this version of R
r
updated 5 days ago by
Pine
▴ 20 • written 12 days ago by
snajafy
• 0
3
votes
3
replies
2.4k
views
How to make a TSS enrichment plot in ATAC-seq analysis?
ATAC
updated 22 days ago by
sp
• 0 • written 22 months ago by
Dan
▴ 180
3
votes
8
replies
1.4k
views
Cellranger count error: Input FASTQ file ended prematurely
scRNA-seq
Cellranger
STARsolo
10X
updated 28 days ago by
swbarnes2
14k • written 9 months ago by
bp22
▴ 80
3
votes
3
replies
229
views
Getting differential ChIP-seq peaks between conditions after calling consensus peaks
MAnorm
ChIP-seq
consensus
peaks
updated 2 days ago by
ATpoint
82k • written 3 days ago by
Alexandra
• 0
3
votes
4
replies
282
views
Would you bother re-mapping RNA-seq data from an old GRCh38 build to a newer version?
RNA-seq
patch
freeze
genome
updated 17 hours ago by
Jeremy Leipzig
22k • written 2 days ago by
Ali
• 0
3
votes
3
replies
201
views
getting exon coordinates
genomics
updated 1 day ago by
Ram
43k • written 1 day ago by
Xbox_27
• 0
3
votes
9
replies
620
views
Is it Acceptable to Have Uniform Quality Scores in a FASTQ File?
FASTQ
updated 23 days ago by
Istvan Albert
100k • written 25 days ago by
Κοσμάς
• 0
3
votes
4
replies
423
views
Why gatk VariantAnnotator required bam and coverage files
gatk
VariantAnnotator
22 days ago by
QX
• 0
3
votes
2
replies
317
views
p-value and Boneferroni adjusted p-value the same in R
Bonferroni
R
Statistics
p-value
Fisher
25 days ago by
kristiewyleung
• 0
3
votes
3
replies
753
views
KissDE and batch effect
kissDE
kissplice
25 days ago by
david.b.rombaut
▴ 10
3
votes
0
replies
154
views
News:
Interested in Spatial Omics?
Bioconductor
Spatial-Omics
Spatial-Transcriptomics
updated 24 days ago by
Ram
43k • written 24 days ago by
carlopecoraro2
★ 2.5k
3
votes
4
replies
4.0k
views
FarmCPU - how to explain the reported 'effect'?
gwas
updated 9 days ago by
chloek88
• 0 • written 5.6 years ago by
Philipp Bayer
8.5k
3
votes
5
replies
402
views
Converting CRAM to FastQ
GATK
samtools
cram
SamToFastq
fastq
14 days ago by
Maverick
▴ 10
3
votes
8
replies
602
views
How to access TCGA samples that were treated with a specific drug?
TCGA
RNA-seq
11 days ago by
Qroid
▴ 40
3
votes
4
replies
3.5k
views
any recommended tools for batch effect and normalization not written in R?
R
RNA-Seq
combat
python
batch-effect
updated 29 days ago by
Ram
43k • written 7.2 years ago by
dyollluap
▴ 310
3
votes
5
replies
352
views
Per base sequence content error in RNAseq analysis
RNA-seq
analysis
updated 25 days ago by
GenoMax
142k • written 26 days ago by
ahmad.sajad4541
• 0
3
votes
7
replies
417
views
FastQC Quality per tile and per sequence behaving strange after using Cutadapt
fastqc
cutadapt
illumina
tile
paired-end
18 days ago by
salias
• 0
3
votes
3
replies
268
views
Genbank vs SRA
ncbi
genbank
genomics
sra
updated 25 days ago by
Mensur Dlakic
★ 27k • written 25 days ago by
c_u
▴ 520
3
votes
4
replies
546
views
biomaRt error for different R version
biomaRt
R
updated 29 days ago by
GenoMax
142k • written 4 weeks ago by
manaswwm
▴ 510
3
votes
1
reply
218
views
Long reads and fixing of mate-pair issues/marking duplicates with samtools
mate-pair
samtools
alignment
updated 4 days ago by
aw7
▴ 300 • written 9 days ago by
Zeng Hao
▴ 40
3
votes
5
replies
344
views
Generating mpileup file using samtools
mpileup
samtools
updated 14 days ago by
Joe
21k • written 15 days ago by
Ruqaiya
• 0
3
votes
3
replies
373
views
genome assembly records not present in assembly_summary.txt
ncbi
bacteria
assembly
updated 21 days ago by
GenoMax
142k • written 22 days ago by
sapuizait
▴ 10
3
votes
3
replies
365
views
Kraken2 database
kraken
microbialdb
database
krakendb
kraken2
updated 4 days ago by
Mathew
▴ 140 • written 7 days ago by
Christopher
• 0
3
votes
2
replies
4.2k
views
Batch effects in sequencing data
batch-effect
updated 29 days ago by
Ram
43k • written 8.8 years ago by
Andrew
▴ 60
3
votes
3
replies
584
views
Korean human genome reference file
GWAS
reference
imputation
29 days ago by
SeoGyun
• 0
3
votes
1
reply
207
views
Question about methylation location
Methylation
WGBS
bisulfide
updated 7 days ago by
dthorbur
★ 2.0k • written 8 days ago by
Eren
• 0
3
votes
2
replies
422
views
Extract protein sequence
fasta
alignment
blast
17 days ago by
anna
▴ 20
2
votes
2
replies
336
views
How to calculate identity percentage between proteins contained in a FASTA file?
protein
FASTA
alignment
updated 23 days ago by
Ram
43k • written 24 days ago by
v.berriosfarias
▴ 140
2
votes
6
replies
5.3k
views
How to avoid over-correction by using harmony or CCA to batch correction in scRNA-seq?
scRNA-seq
R
seurat
harmony
batch-effect
updated 29 days ago by
Ram
43k • written 3.8 years ago by
Lukadon77
• 0
2
votes
4
replies
270
views
Can 5' and 3' scRNAseq be processed with the same pipeline?
singlecell
seurat
10XGenomics
scRNAseq
updated 2 days ago by
yura.grabovska
▴ 90 • written 2 days ago by
ev97
▴ 20
2
votes
2
replies
197
views
genome finishing
finishing
genome
updated 2 days ago by
nd48
▴ 20 • written 2 days ago by
trezini
• 0
2
votes
2
replies
432
views
differential gene expression analysis when not all samples have an untreated counterpart
differential-expression
edgeR
29 days ago by
nhaus
▴ 360
2
votes
3
replies
848
views
Issues with Mixture file when using CIBERSORTx
Deconvolution
CIBERSORTx
updated 13 days ago by
vjanve
• 0 • written 7 months ago by
mateomejias
• 0
2
votes
7
replies
1.4k
views
6 follow
Differential Expression using Isoseq-supplemented reference transcriptome
RNA-Seq
Salmon
Isoseq
updated 19 days ago by
Gordon Smyth
★ 7.2k • written 8 months ago by
Calum
▴ 10
2
votes
2
replies
204
views
Genome Visualization Tools
bacterial
genome
updated 3 days ago by
GenoMax
142k • written 3 days ago by
dlera.lozano
▴ 10
753 results • Page
3 of 16
Recent Votes
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Comment: ChatGPT optimized for bioinformatics questions
C: How can I perform Differential expression analysis with just one control and one
C: How can I perform Differential expression analysis with just one control and one
C: How can I perform Differential expression analysis with just one control and one
How can I perform Differential expression analysis with just one control and one cancer sample?
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Recent Replies
Comment: how to treat the replicates while performing WGCNA
by
mavy
▴ 10
Thank you so much for your response . Really appreciate it. I will try the way you mentioned and will get back if I have any query
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
hophuquy0944
• 0
i have the same error, i used high performance computer, here is my code to set memory. srun --nodes=1 --ntasks=1 --cpus-per-task=24 -…
Comment: Overlapping Ranges within Granges object
by
Alex Reynolds
35k
Yes, `bedmap` will perform operations on one or two BED files.
Comment: B allele frequency (BAF)
by
aidangcruickshank
▴ 10
Apologies for resurrecting this post, but any idea what that functions "regions" paramater takes? Would it be a GRanges object? The documen…
Comment: How to handle duplicated genes in TCGA data?
by
Ngrin
• 0
Thanks @txema.heredia.The tool I am going to use only accepts gene symbols. This is the reason. So I cannot use ENS IDs.
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by
swbarnes2
14k
This is a rather small experiment, I don't know that you can establish a meaningful baseline for each patient with a single pre sample, and…
Comment: GG Sankey plot
by
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4.2k
@bk11 i changed this comment to an answer. if you disagree please let me know. thanks for sharing your knowledge. VAL
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation
by
hannes.bongartz
• 0
Thanks for the input. Unfortunately, that didn't help either. I appreciate any other tips. Thank you
Answer: GG Sankey plot
by
bk11
★ 2.5k
You need to change your data table into a 'long' format. You can do something like this- GOs_childs_recursive <- GOs_childs_recursive …
Answer: Trimming tool
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ntsopoul
▴ 60
I use Trim Galore which automatically recognizes adaptors. https://github.com/FelixKrueger/TrimGalore Here is the script I am using for…
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GenoMax
142k
There are plenty. `bbduk.sh` from BBMap suite (https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbduk-guide/ )…
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation
by
bk11
★ 2.5k
Please check out [in this link.][1] [1]: https://github.com/jokergoo/ComplexHeatmap/issues/349
Comment: Reconstruction of locus, order contigs
by
dthorbur
★ 2.0k
[Here](https://www.biostars.org/p/9544689/) is a forum post that may answer your question.
Comment: how to treat the replicates while performing WGCNA
by
andres.firrincieli
3.6k
> 1) I do not want to merge the MEs rather I asked about replicates, as > some replicates of same sample are showing different behavior for…
Comment: How to systematically check if a bam file is truncated
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alanh
▴ 170
For more details about what `samtools quickcheck` actually checks for, add a few `-v`'s to the command line. $ samtools quickcheck -…
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