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1,101 results • Page 3 of 23
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5
votes
4
replies
671
views
How to compare the quality of assemblies
nextdenovo assembly hifiasm pacbio
8 days ago by kirillkirilenko ▴ 40
5
votes
3
replies
332
views
Best genome browser for manual curation of gene structure(s)?
structure gene
updated 20 days ago by ★ 3.8k • written 21 days ago by ★ 5.3k
5
votes
13
replies
9.2k
views
8 follow
biomaRt: Timeout on getBM().
r biomart ensembl
updated 20 days ago by ★ 2.0k • written 2.8 years ago by ▴ 40
5
votes
3
replies
246
views
6 follow
Integrate transcriptomic data and proteomics data.
OMICS
updated 2 days ago by ★ 1.2k • written 2 days ago by • 0
5
votes
3
replies
346
views
Problems with Nextflow to run NanoRtax Pipeline
NanoRtax Nextflow Nanopore
updated 27 days ago by 6.4k • written 28 days ago by • 0
5
votes
3
replies
405
views
Ensembl assembly choice for DNA reference with no combined primary assembly
alignment HISAT2 RNA-Seq ensembl Assembly
updated 20 days ago by 142k • written 20 days ago by ▴ 20
5
votes
13
replies
1.3k
views
Tutorial: Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
R Ubuntu Linux Bioconductor Rstudio
updated 11 days ago by 82k • written 12 days ago by ★ 1.7k
5
votes
3
replies
294
views
Forum: Ideal PC configurations and operating system for bioinformatics laboratory
PC
updated 8 days ago by 142k • written 8 days ago by • 0
5
votes
6
replies
7.3k
views
scatter plot, aov()
aov scatter-plot anova
updated 15 days ago by 43k • written 3.2 years ago by ▴ 170
5
votes
4
replies
343
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
16 days ago by Spring • 0
5
votes
6
replies
453
views
Programmatically retrieving positions of protein active site residues
Uniprot PDB Proteins
updated 1 day ago by ▴ 760 • written 2 days ago by ▴ 40
5
votes
5
replies
7.2k
views
Converting scRNA-Seq to Bulk-RNASeq
scRNASeq bulk-RNASeq RNA-Seq single-cell
updated 21 days ago by • 0 • written 3.8 years ago by ★ 1.8k
5
votes
5
replies
872
views
Blacklist for bacterial genome [ChIPseq]?
ChIPseq Blacklist
updated 19 days ago by 43k • written 10 months ago by ▴ 30
5
votes
4
replies
676
views
DEG analysis of RNA-seq data across multiple tissues and two conditions
RNA-seq EdgeR DEGs DESeq2
13 days ago by BioinfGuru ★ 1.7k
5
votes
4
replies
2.8k
views
genefu for PAM50 prediction
RNA-Seq breast cancer subtyping
updated 15 days ago by ▴ 70 • written 5.7 years ago by ▴ 50
5
votes
5
replies
564
views
NCBI MEGABLAST versus UCSC BLAT
blast blat alignment megablast
updated 22 days ago by ▴ 580 • written 23 days ago by ▴ 40
5
votes
12
replies
1.6k
views
Subbmission Data
RNA-seq
updated 29 days ago by 43k • written 14 months ago by ▴ 50
5
votes
7
replies
2.7k
views
DESeq2 for differential gene expression on GTEx dataset
differential-gene-expression RNA-Seq GTex DESeq2
updated 22 days ago by 43k • written 6.4 years ago by ▴ 10
5
votes
14
replies
1.0k
views
Not getting any modification calls in nanopore reads with dorado basecaller
mofications dorado basecalling nanopore methylation
updated 20 days ago by 142k • written 5 weeks ago by ▴ 20
5
votes
2
replies
1.0k
views
How to perform batch correction when we have only single condition?
sva combat batch-effect DESeq2
updated 15 days ago by 43k • written 3.8 years ago by ▴ 680
5
votes
5
replies
2.1k
views
batch effect in RNAseq analysis using tophat cufflinks pipeline
RNA-Seq tophat batch-effect cufflinks
updated 14 days ago by 43k • written 5.3 years ago by • 0
5
votes
2
replies
672
views
DESeq2- How to design data for multiple comparisons?
Differential-Gene-Expression RNA-Seq DESeq2 R
updated 22 days ago by 43k • written 3.6 years ago by • 0
5
votes
20
replies
4.2k
views
Differential gene expression from RNAseq data. Before or after annotation?
differential-gene-expression RNA-seq
updated 22 days ago by 43k • written 6.2 years ago by ▴ 90
5
votes
2
replies
2.6k
views
How do you evaluate the effectiveness of the batch effect algorithm?
Batch-Effect
updated 13 days ago by 43k • written 9.1 years ago by ▴ 110
5
votes
16
replies
659
views
How many reads for WGS Sequencing?
WGS Bacterial-Genomics
3 days ago by Ruqaiya • 0
5
votes
6
replies
422
views
7 follow
Seeking Help with Unexpected MA Plot Output
MAplot RNAseq Rstudio
updated 29 days ago by 100k • written 4 weeks ago by • 0
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 22 days ago by 43k • written 2.7 years ago by ▴ 170
4
votes
2
replies
312
views
Forum: Bioinformatics: Where do I start
Sequencing
updated 15 days ago by 43k • written 15 days ago by ▴ 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 43k • written 6.3 years ago by ▴ 260
4
votes
2
replies
394
views
Missing protein (VEGF-A) in String db
VGFA stringdb
updated 6 days ago by • 0 • written 12 weeks ago by ▴ 20
4
votes
11
replies
754
views
Redirection of Duplicate PMIDs
pubmed pmid
updated 8 days ago by 4.2k • written 9 days ago by • 0
4
votes
5
replies
272
views
High Malat-1 expression in single cell data
cell analysis single
updated 2 days ago by ★ 5.9k • written 2 days ago by ▴ 10
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
4
replies
431
views
How do I install plink2 on a mac?
plink2 plink
updated 17 days ago by 11k • written 19 days ago by ▴ 10
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 ▴ 80 • written 20 days ago by ▴ 850
4
votes
9
replies
590
views
variant calling
variant-calling
updated 28 days ago by 43k • written 29 days ago by • 0
4
votes
5
replies
3.4k
views
Please clarify me about countOverlaps()?
RNA-Seq countOverlaps R
updated 15 days ago by 43k • written 6.3 years ago by ★ 1.9k
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
6
replies
2.0k
views
RNA-Seq DGE: Evaluate model quality
differential-gene-expression RNA-Seq deseq2
updated 22 days ago by 43k • written 6.2 years ago by ★ 1.6k
4
votes
4
replies
14k
views
Heatmap with custom gene labels annotated on the rows
differential-gene-expression RNAseq heatmap
updated 22 days ago by 43k • written 4.7 years ago by ▴ 370
4
votes
2
replies
3.8k
views
DESeq2 design and batch effect
RNA-Seq batch-effect DESeq2 Salmon
updated 13 days ago by 43k • written 6.5 years ago by ▴ 30
4
votes
8
replies
630
views
Create a new bed file with all pairwise combinations between two other bed files, based on bp distance
SNPs BED eqtl bedtools
updated 5 days ago by 35k • written 6 days ago by ▴ 10
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
6
replies
848
views
bwa mem hangs after a few thousand reads
bwa alignment variant-calling bwa-mem
updated 29 days ago by 43k • written 5 months ago by ▴ 30
4
votes
2
replies
1.2k
views
Tool: Introducing Cramino: a *fast* QC tool for long reads
long-read nanopore pacbio
updated 26 days ago by 43k • written 18 months ago by 47k
4
votes
7
replies
581
views
DESeq2 Multifactor Design
RNA-seq DESeq2
updated 18 days ago by 43k • written 19 days ago by ▴ 20
4
votes
7
replies
670
views
7 follow
Heatmap and rna-seq
RNA-Seq Heatmap
updated 5 days ago by ★ 5.9k • written 9 days ago by ▴ 10
4
votes
2
replies
343
views
Assume "yes" as the answer to any prompts with bioconda
docker container bioconda
updated 13 days ago by 8.6k • written 13 days ago by ▴ 20
4
votes
5
replies
543
views
Getting refseq assembly accession numbers from list of species names
haystac accession refseq assembly ncbi
updated 27 days ago by 142k • written 27 days ago by • 0
4
votes
6
replies
3.9k
views
Correcting for batch effect in RNA-seq data
RNA-Seq batch-effect
updated 14 days ago by 43k • written 4.8 years ago by ▴ 30
1,101 results • Page 3 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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Recent Replies
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
Comment: How to perform single cell multimodal integration using Seurat for Geo datasets by ATpoint 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 liorglic ★ 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…
Answer: Bacterial plasmid analysis by Mensur Dlakic ★ 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 …
Comment: POSSUM not working due to incompatible pssm file by rianna.collins • 0
Thank you so much. I'm new to this and didn't realise there was a code option.
Answer: Is there a way to increase the automatic label text size in Cytoscape? by Scooter ▴ 280
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…
Answer: Basic stats in hierfstat by mdav • 0
Hi Zoe, did you find an answer for this? I am also getting the same error.
Comment: GATK won't produce figures while analyzing covariates to generate 'recal_plots.p by GenoMax 141k
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…
Comment: Post-imputation plot by kl ▴ 10
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…
Comment: Bacterial plasmid analysis 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…
Comment: Bacterial plasmid analysis by GenoMax 141k
Can you classify the plasmids based on function (resistance genes they are carrying or some other criteria). Sizes above are indicating a w…
Comment: DESeq2 processing problems by ATpoint 82k
Initially posted here https://support.bioconductor.org/p/9158036/ where I suggested to put code and data and noted that GEOquery returns ar…
Answer: Post-imputation plot by LChart 3.9k
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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