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1,101 results • Page
4 of 23
Sort: Votes
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Votes
Replies
4
votes
7
replies
484
views
To get p-values for the TPM
P-value
TPM
RSEM
updated 7 days ago by
dsull
★ 5.9k • written 8 days ago by
VITALA
• 0
4
votes
9
replies
2.7k
views
Tool:
CANEapp, a user-friendly application for automated next generation transcriptomic data analysis
RNA-Seq
written 8.3 years ago by
dvelmeshev
• 0
4
votes
6
replies
848
views
bwa mem hangs after a few thousand reads
bwa
alignment
variant-calling
bwa-mem
updated 29 days ago by
Ram
43k • written 5 months ago by
cee28
▴ 30
4
votes
3
replies
10k
views
short and long reads
long-reads
Assembly
short-reads
updated 26 days ago by
Ram
43k • written 10.0 years ago by
midox
▴ 290
4
votes
5
replies
1.9k
views
which package should be selected for differential gene expression analysis
Differential-gene-expression
RNA-Seq
updated 22 days ago by
Ram
43k • written 5.5 years ago by
lkianmehr
▴ 100
4
votes
4
replies
475
views
Error Codes in Snakemake
python
snakemake
26 days ago by
888pea
▴ 10
4
votes
3
replies
2.2k
views
The result of differential gene expression analysis should be extracted based on adj.p.value ?
limma
microarray
bioconductor
R
updated 15 days ago by
Ram
43k • written 6.3 years ago by
Raheleh
▴ 260
4
votes
4
replies
431
views
How do I install plink2 on a mac?
plink2
plink
updated 17 days ago by
zx8754
11k • written 19 days ago by
emilija.romic
▴ 10
4
votes
6
replies
1.5k
views
CompressedGRangesList don't have seqLengths: BiocParallel errors: Error in covRleFromGR(x, weight = weight, ignore.strand = ignore.strand): Seqlength…
gff3
GenomicRanges
ORFik
GenomicFeatures
updated 16 days ago by
GenoMax
142k • written 15 months ago by
Estefania
▴ 30
4
votes
2
replies
312
views
Forum:
Bioinformatics: Where do I start
Sequencing
updated 15 days ago by
Ram
43k • written 15 days ago by
Adi
▴ 10
4
votes
11
replies
754
views
Redirection of Duplicate PMIDs
pubmed
pmid
updated 8 days ago by
LauferVA
4.2k • written 9 days ago by
dominickd
• 0
4
votes
2
replies
3.8k
views
DESeq2 design and batch effect
RNA-Seq
batch-effect
DESeq2
Salmon
updated 13 days ago by
Ram
43k • written 6.5 years ago by
georgewwp
▴ 30
4
votes
2
replies
245
views
Trying to write bwa mem -> samtools view -> samtools sort loop
bwa
samtools
mapping
genome
updated 27 days ago by
Pierre Lindenbaum
161k • written 27 days ago by
Lee
• 0
4
votes
9
replies
2.1k
views
Legend and hap files for imputation with 38 build
reference
38build
impute
imputation
2 days ago by
anna
▴ 20
4
votes
3
replies
7.6k
views
Genotype representation with 0, 1, 2 - what do they mean?
genotype
representation
phasing
imputation
gwas
updated 27 days ago by
far
• 0 • written 5.9 years ago by
Volka
▴ 180
4
votes
2
replies
394
views
Missing protein (VEGF-A) in String db
VGFA
stringdb
updated 6 days ago by
shalespringer
• 0 • written 12 weeks ago by
Phenylananin
▴ 20
4
votes
7
replies
581
views
DESeq2 Multifactor Design
RNA-seq
DESeq2
updated 18 days ago by
Ram
43k • written 19 days ago by
AHerik
▴ 20
4
votes
4
replies
484
views
Why number of interactions decreased in current string database for plasmodium
string
interactions
ppi
updated 19 days ago by
damian.szk
▴ 80 • written 20 days ago by
rohitsatyam102
▴ 850
4
votes
6
replies
2.0k
views
RNA-Seq DGE: Evaluate model quality
differential-gene-expression
RNA-Seq
deseq2
updated 22 days ago by
Ram
43k • written 6.2 years ago by
firestar
★ 1.6k
4
votes
0
replies
876
views
Tool:
PyComplexHeatmap: a Python package to visualize multimodal genomics data
visualization
Python
ComplexHeatmap
PyComplexHeatmap
21 days ago by
Wubin
▴ 40
4
votes
5
replies
3.4k
views
Please clarify me about countOverlaps()?
RNA-Seq
countOverlaps
R
updated 15 days ago by
Ram
43k • written 6.3 years ago by
seta
★ 1.9k
4
votes
2
replies
286
views
How to use limma to find differentially expressed genes in response to a continuous variable
limma
voom
R
2 days ago by
pairedttest
▴ 10
4
votes
0
replies
121
views
Herald:
The Biostar Herald for Monday, April 29, 2024
herald
2 days ago by
Biostar
2.7k
4
votes
4
replies
432
views
Tutorial:
how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix
RNAseq
R
updated 4 days ago by
BioinfGuru
★ 1.7k • written 7 days ago by
Ming Tommy Tang
★ 3.9k
3
votes
3
replies
348
views
Disrupting a gene interaction network
cytohubba
cytoscape
sequences
mRNA
20 days ago by
george
• 0
3
votes
6
replies
1.5k
views
edgeR FDR always 1
FDR
differential-gene-expression
edgeR
miRNA
updated 22 days ago by
Ram
43k • written 4.9 years ago by
AngAdd
▴ 20
3
votes
6
replies
2.4k
views
How to adjust by multiple variables using ComBat-Seq?
CombatSeq
combat
rna-seq
sva
batch-effect
updated 15 days ago by
Ram
43k • written 21 months ago by
ev97
▴ 20
3
votes
1
reply
2.2k
views
Maximum Number of Gene in a DESeq2 and edgeR
Differential-Gene-Expression
EdgeR
DESeq2
updated 22 days ago by
Ram
43k • written 8.1 years ago by
rieza.aprianto
▴ 10
3
votes
4
replies
480
views
biomaRt error for different R version
biomaRt
R
updated 13 days ago by
GenoMax
142k • written 15 days ago by
manaswwm
▴ 510
3
votes
3
replies
441
views
trouble using sequenceTubeMap in chromium installed on WSL
vg
15 days ago by
ayushm64
• 0
3
votes
2
replies
2.1k
views
Batch effect correction - miRNA sequencing - DESeq2
Batch-effect
DESeq2
miRNA-Seq
updated 15 days ago by
Ram
43k • written 5.5 years ago by
prekrish
• 0
3
votes
6
replies
8.4k
views
RNA-seq, EdgeR and batch effects
RNA-Seq
removeBatchEffect
edgeR
batch-effect
updated 15 days ago by
Ram
43k • written 9.3 years ago by
Ekarl2
▴ 120
3
votes
6
replies
11k
views
List of species in RepeatMasker Tool (species parameter)
RepeatMasker
Masking
updated 15 days ago by
Bioinfotec
▴ 10 • written 7.6 years ago by
nut_B
▴ 10
3
votes
6
replies
688
views
Ciriquant not configuring hisat2 indexed files
ciriquant
10 days ago by
Atul K.
• 0
3
votes
3
replies
2.4k
views
How to make a TSS enrichment plot in ATAC-seq analysis?
ATAC
updated 6 days ago by
sp
• 0 • written 22 months ago by
Dan
▴ 180
3
votes
4
replies
410
views
Genome completeness and contamination: CheckM vs CheckM2
genome-completeness
contamination
27 days ago by
beacamara
• 0
3
votes
2
replies
4.2k
views
Batch effects in sequencing data
batch-effect
updated 13 days ago by
Ram
43k • written 8.7 years ago by
Andrew
▴ 60
3
votes
1
reply
235
views
Seurat merge and batch correction
Seurat
updated 8 days ago by
Ram
43k • written 9 days ago by
sooni
▴ 20
3
votes
6
replies
900
views
Any problem re-using last year's RNA-Seq data in this year's analysis?
RNA-Seq
batch-effect
updated 15 days ago by
Ram
43k • written 3.7 years ago by
oakhamwolf
▴ 20
3
votes
2
replies
1.0k
views
Can I take 'organ type' as a batch effect and use ComBat to remove organ dependent variations?
RNA-Seq
Cross-Species
SVA
ComBat
Batch-Effect
updated 15 days ago by
Ram
43k • written 4.7 years ago by
rodguinea
• 0
3
votes
7
replies
542
views
Artificial deletion in bam
bam
updated 26 days ago by
Zhenyu Zhang
★ 1.2k • written 27 days ago by
enee
▴ 10
3
votes
5
replies
594
views
SLURM submission problem: Indexing the Reference Genome is not done in STAR
align
RNA-Seq
linux
STAR
10 days ago by
n_navy
• 0
3
votes
8
replies
4.1k
views
Using FPKM and TPM values for batch correction for Single Cell RNA-Seq
fpkm
scRNA-seq
RNA-Seq
tpm
batch-effect
updated 13 days ago by
Ram
43k • written 4.6 years ago by
hkarakurt
▴ 180
3
votes
1
reply
878
views
Fisher exact test in R package
Fisher-test
updated 29 days ago by
Ram
43k • written 2.9 years ago by
Nuglozeh
▴ 10
3
votes
2
replies
309
views
Seeking Guidance on How to Annotate Unusual Cell Populations in Single-Cell Data
Transcriptomics
Single-Cell
updated 26 days ago by
Ram
43k • written 8 weeks ago by
Daddy
▴ 20
3
votes
3
replies
228
views
TMM normalization with DESeq2
RNA-seq
DESeq2
updated 29 days ago by
Ram
43k • written 29 days ago by
marco.barr
▴ 90
3
votes
3
replies
535
views
How to run BRIG on Ubuntu 22?
BRIG
Ubuntu
updated 28 days ago by
Reno
• 0 • written 3 months ago by
marongiu.luigi
▴ 710
3
votes
7
replies
500
views
Integration of transcriptomics and proteomics: difficult matching names
rna-seq
tmt
nomenclature
proteomics
15 days ago by
ntsopoul
▴ 60
3
votes
5
replies
1.4k
views
Removing Batch effect that is the same as condition - DESEq2
RNA-Seq
batch-effect
DESeq2
updated 23 days ago by
Ram
43k • written 3.9 years ago by
annamariabugaj
• 0
3
votes
1
reply
276
views
how to change the gene header names in a fasta file?
fasta
bioawk
awk
seqkit
updated 20 days ago by
Ram
43k • written 20 days ago by
rj.rezwan
• 0
1,101 results • Page
4 of 23
Recent Votes
Answer: Bacterial plasmid analysis
Answer: Bacterial plasmid analysis
Discrepancy in read counts from fastq
R: Unable to use analyzeFeatures because argument is not a vector
Comment: Odd alignment question/finding
Comment: POSSUM not working due to incompatible pssm file
Comment: Can't install AnnotationHub
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Answer: Subsetting and merging back Seurat Object brings different results
by
Bine
▴ 60
Noone has an idea? Thank you!
Answer: Bacterial plasmid analysis
by
shenwei356
8.5k
My colleague has an unpublished tool for plasmid analysis (clustering), and it has really good results. You might have a try. https://githu…
Comment: Odd alignment question/finding
by
ATpoint
82k
bwa mem is not fully deterministic, see from the developer: https://www.biostars.org/p/238628/#238817
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by
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82k
It's funny that you ask because the paper that these data were used for is called `Integrated analysis of multimodal single-cell data` from…
Comment: Odd alignment question/finding
by
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★ 1.4k
I can't come up with an explanation, but two things you can try for debugging are: 1) look at the fastp stats - do they add up and make sen…
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by
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★ 27k
If you put all your sequences in separate files but in the same directory, this program will build a cladogram based on average nucleotide …
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by
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Thank you so much. I'm new to this and didn't realise there was a code option.
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Greetings, Are you saying that you can't use the size setting in the style tab? That should certainly work, as should the label size se…
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Your cluster may be missing libraries etc to create the PDF plots (this looks like a cluster job submission) on your cluster. Did you check…
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Ok yes I think my thought was that given these errors, I could remove the mismatches and flip the alleles which seem to need flipping based…
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by
nicole.kavanagh
• 0
I think I will perhaps use their predominant PlasmidFinder type to group plasmids together and create separate core phylogenies for each as…
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Can you classify the plasmids based on function (resistance genes they are carrying or some other criteria). Sizes above are indicating a w…
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Initially posted here https://support.bioconductor.org/p/9158036/ where I suggested to put code and data and noted that GEOquery returns ar…
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I agree that some need to be flipped (A/T and C/G where your panel frequency is 1 - ref panel frequency). There are other variants which yo…
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