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1,000 results • Page
3 of 20
Sort: Votes
Rank
Views
Votes
Replies
5
votes
2
replies
664
views
DESeq2- How to design data for multiple comparisons?
Differential-Gene-Expression
RNA-Seq
DESeq2
R
updated 15 days ago by
Ram
43k • written 3.6 years ago by
ginny
• 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
5
votes
6
replies
7.3k
views
scatter plot, aov()
aov
scatter-plot
anova
updated 8 days ago by
Ram
43k • written 3.2 years ago by
Rob
▴ 170
5
votes
2
replies
1.0k
views
How to perform batch correction when we have only single condition?
sva
combat
batch-effect
DESeq2
updated 8 days ago by
Ram
43k • written 3.8 years ago by
svp
▴ 680
5
votes
14
replies
959
views
Not getting any modification calls in nanopore reads with dorado basecaller
mofications
dorado
basecalling
nanopore
methylation
updated 14 days ago by
GenoMax
141k • written 5 weeks ago by
njornet
▴ 20
5
votes
2
replies
2.6k
views
How do you evaluate the effectiveness of the batch effect algorithm?
Batch-Effect
updated 6 days ago by
Ram
43k • written 9.1 years ago by
chengzhao41
▴ 110
5
votes
3
replies
1.0k
views
How to normalize long-read RNA-seq data for comparison with short-reads
RNAseq
long-reads
normalization
short-reads
updated 22 days ago by
rpolicastro
13k • written 15 months ago by
Bernardo
▴ 20
5
votes
8
replies
3.7k
views
Many Differentially expressed genes but few GO terms
differential-gene-expression
RNA-seq
gene-ontology
updated 15 days ago by
Ram
43k • written 6.5 years ago by
firestar
★ 1.6k
5
votes
3
replies
317
views
Best genome browser for manual curation of gene structure(s)?
structure
gene
updated 13 days ago by
cmdcolin
★ 3.8k • written 14 days ago by
William
★ 5.3k
5
votes
4
replies
2.2k
views
How do we process Kallisto output (continuous real values) for DESEQ2 analysis (which strictly require discrete count values)?
read-counts
DESEQ2
differential-gene-expression
kallisto
updated 15 days ago by
Ram
43k • written 2.7 years ago by
mrj
▴ 170
5
votes
5
replies
7.2k
views
Converting scRNA-Seq to Bulk-RNASeq
scRNASeq
bulk-RNASeq
RNA-Seq
single-cell
updated 14 days ago by
veldahan86
• 0 • written 3.8 years ago by
Assa Yeroslaviz
★ 1.8k
5
votes
5
replies
5.5k
views
beagle 4 exception: Duplicate marker
vcf
IBD
plink
beagle
updated 29 days ago by
Ram
43k • written 9.4 years ago by
galbarel
▴ 10
5
votes
12
replies
1.5k
views
Subbmission Data
RNA-seq
updated 23 days ago by
Ram
43k • written 14 months ago by
GiV17
▴ 50
5
votes
3
replies
704
views
Illumina reads preprocessing best practice for snp calling applications
Illumina
snp
updated 6 days ago by
Enrique
• 0 • written 9 months ago by
Denis
▴ 310
5
votes
4
replies
307
views
I'm new to cell ranger. Can single cells prepared with a protocol other than the 10x genomics protocol not be processed with cell ranger?
cellranger
scRNA-seq
10x
9 days ago by
Spring
• 0
5
votes
13
replies
9.1k
views
8 follow
biomaRt: Timeout on getBM().
r
biomart
ensembl
updated 14 days ago by
Mike Smith
★ 2.0k • written 2.8 years ago by
lincaijin1994
▴ 40
5
votes
5
replies
536
views
NCBI MEGABLAST versus UCSC BLAT
blast
blat
alignment
megablast
updated 15 days ago by
joe
▴ 510 • written 16 days ago by
a615ebfb
▴ 40
5
votes
5
replies
2.1k
views
batch effect in RNAseq analysis using tophat cufflinks pipeline
RNA-Seq
tophat
batch-effect
cufflinks
updated 7 days ago by
Ram
43k • written 5.3 years ago by
yff
• 0
5
votes
13
replies
1.1k
views
Tutorial:
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
R
Ubuntu
Linux
Bioconductor
Rstudio
updated 5 days ago by
ATpoint
82k • written 6 days ago by
BioinfGuru
★ 1.7k
5
votes
7
replies
2.7k
views
DESeq2 for differential gene expression on GTEx dataset
differential-gene-expression
RNA-Seq
GTex
DESeq2
updated 15 days ago by
Ram
43k • written 6.4 years ago by
vikram
▴ 10
5
votes
20
replies
4.2k
views
Differential gene expression from RNAseq data. Before or after annotation?
differential-gene-expression
RNA-seq
updated 15 days ago by
Ram
43k • written 6.2 years ago by
pablo61991
▴ 90
5
votes
3
replies
320
views
Problems with Nextflow to run NanoRtax Pipeline
NanoRtax
Nextflow
Nanopore
updated 21 days ago by
colindaven
6.4k • written 21 days ago by
kerianaleerivera
• 0
5
votes
4
replies
616
views
How to compare the quality of assemblies
nextdenovo
assembly
hifiasm
pacbio
1 day ago by
kirillkirilenko
▴ 40
5
votes
3
replies
385
views
Ensembl assembly choice for DNA reference with no combined primary assembly
alignment
HISAT2
RNA-Seq
ensembl
Assembly
updated 13 days ago by
GenoMax
141k • written 13 days ago by
AHerik
▴ 20
5
votes
4
replies
618
views
DEG analysis of RNA-seq data across multiple tissues and two conditions
RNA-seq
EdgeR
DEGs
DESeq2
6 days ago by
BioinfGuru
★ 1.7k
5
votes
4
replies
2.8k
views
genefu for PAM50 prediction
RNA-Seq
breast cancer
subtyping
updated 8 days ago by
hamarillo
▴ 70 • written 5.7 years ago by
silviajserrano
▴ 50
5
votes
5
replies
848
views
Blacklist for bacterial genome [ChIPseq]?
ChIPseq
Blacklist
updated 12 days ago by
Ram
43k • written 10 months ago by
Emily Wasson
▴ 30
5
votes
6
replies
391
views
7 follow
Seeking Help with Unexpected MA Plot Output
MAplot
RNAseq
Rstudio
updated 22 days ago by
Istvan Albert
100k • written 23 days ago by
Pumla
• 0
4
votes
4
replies
14k
views
Heatmap with custom gene labels annotated on the rows
differential-gene-expression
RNAseq
heatmap
updated 15 days ago by
Ram
43k • written 4.7 years ago by
bioinforesearchquestions
▴ 370
4
votes
5
replies
349
views
merging tetraploid vcf files through bcftools
vcf
bcftools
23 days ago by
analyst
▴ 30
4
votes
2
replies
316
views
Assume "yes" as the answer to any prompts with bioconda
docker
container
bioconda
updated 7 days ago by
Juke34
8.5k • written 7 days ago by
njornet
▴ 20
4
votes
9
replies
1.1k
views
Error in openning FastQC
fastqc
igv
updated 27 days ago by
GenoMax
141k • written 8 months ago by
huynhthienphai
• 0
4
votes
4
replies
393
views
How do I install plink2 on a mac?
plink2
plink
updated 10 days ago by
zx8754
11k • written 12 days ago by
emilija.romic
▴ 10
4
votes
7
replies
2.4k
views
Batch effects vs biological variables
Batch-effect
DESeq2
combat_seq
updated 16 days ago by
Ram
43k • written 3.7 years ago by
l.uva
▴ 20
4
votes
4
replies
461
views
Error Codes in Snakemake
python
snakemake
19 days ago by
888pea
▴ 10
4
votes
2
replies
1.7k
views
How to convert SAM/BAM file to GTF/GFF file?
GTF
SAM
BAM
GFF
minimap2
updated 8 days ago by
Dr.Animo
▴ 130 • written 12 months ago by
BioinfoBee
• 0
4
votes
11
replies
487
views
Redirection of Duplicate PMIDs
pubmed
pmid
updated 1 day ago by
LauferVA
4.2k • written 2 days ago by
dominickd
• 0
4
votes
2
replies
225
views
Trying to write bwa mem -> samtools view -> samtools sort loop
bwa
samtools
mapping
genome
updated 20 days ago by
Pierre Lindenbaum
161k • written 20 days ago by
Lee
• 0
4
votes
9
replies
568
views
variant calling
variant-calling
updated 21 days ago by
Ram
43k • written 23 days ago by
dalibenam64
• 0
4
votes
4
replies
463
views
Why number of interactions decreased in current string database for plasmodium
string
interactions
ppi
updated 13 days ago by
damian.szk
▴ 70 • written 13 days ago by
rohitsatyam102
▴ 840
4
votes
3
replies
10k
views
short and long reads
long-reads
Assembly
short-reads
updated 19 days ago by
Ram
43k • written 9.9 years ago by
midox
▴ 290
4
votes
6
replies
2.0k
views
RNA-Seq DGE: Evaluate model quality
differential-gene-expression
RNA-Seq
deseq2
updated 15 days ago by
Ram
43k • written 6.2 years ago by
firestar
★ 1.6k
4
votes
4
replies
330
views
How to fetch published paper of a BioProject
BioProject
pumbed
NGS
16 days ago by
Morteza
• 0
4
votes
7
replies
590
views
UK biobank versus Genomics England
WGS
DRAGEN
GenomicsEngland
UK-BRAP
vcf
written 12 weeks ago by
zizigolu
★ 4.3k
4
votes
6
replies
832
views
bwa mem hangs after a few thousand reads
bwa
alignment
variant-calling
bwa-mem
updated 23 days ago by
Ram
43k • written 4 months ago by
cee28
▴ 30
4
votes
11
replies
1.3k
views
Paired layout, but one fastq file
fastq
updated 28 days ago by
GenoMax
141k • written 13 months ago by
Andy
▴ 120
4
votes
6
replies
1.4k
views
CompressedGRangesList don't have seqLengths: BiocParallel errors: Error in covRleFromGR(x, weight = weight, ignore.strand = ignore.strand): Seqlength…
gff3
GenomicRanges
ORFik
GenomicFeatures
updated 10 days ago by
GenoMax
141k • written 15 months ago by
Estefania
▴ 30
4
votes
2
replies
278
views
Forum:
Bioinformatics: Where do I start
Sequencing
updated 8 days ago by
Ram
43k • written 9 days ago by
Adi
▴ 10
4
votes
13
replies
862
views
RNAseq of primary tumor and metastases in two different organ
metastases
RNA-seq
DEG
R
updated 8 days ago by
BioinfGuru
★ 1.7k • written 14 days ago by
matteo.levorato
• 0
4
votes
9
replies
2.6k
views
Tool:
CANEapp, a user-friendly application for automated next generation transcriptomic data analysis
RNA-Seq
written 8.2 years ago by
dvelmeshev
• 0
1,000 results • Page
3 of 20
Recent Votes
What is the difference between HaplotypeCaller and UnifiedGenotyper?
What is the difference between HaplotypeCaller and UnifiedGenotyper?
RSeQC Output from infer_experiment.py - what does it mean?
ScRNAseq-How to correctly choose cell type marker genes
ScRNA data question
Comment: SRA to BAM
Answer: What Is A "Spot" In Sra Format
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Comment: GAPIT p-value significance threshold
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Hi, I was wondering if you have found a solution to this? Thanks!
Comment: PCA plot
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▴ 170
cross posted in bioconductor. [https://support.bioconductor.org/p/9157968/][1] [1]: https://support.bioconductor.org/p/9157968/
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★ 2.3k
Which normalization method did you use for your data? I am guessing you had used SCTransform normalization for your data. Can you plot usin…
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by
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• 0
I think the coverage could also computed from bam file itself, but let say I do not include the coverage, do you have any idea why it needs…
Comment: Is it possible to get a list of representative genomes from a past RefSeq releas
by
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141k
I am moving my answer to a comment. At this point you should email NCBI help desk and ask them this question. If you get an answer then ple…
Comment: Figures are disappeared from html report of SnpEff
by
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161k
the javascript in your html is deprecated or your firefox is just tool old.
Comment: Why gatk VariantAnnotator required bam and coverage files
by
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161k
> I would like to ask why they may require the bam file for this function? hum.. if you want to add the coverage, where do you think gatk …
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
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★ 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…
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