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760 results • Page 2 of 16
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5
votes
7
replies
489
views
RNA seq analysis
DESeq RNA-seq
2 days ago by Jacek ▴ 20
5
votes
2
replies
439
views
Missing protein (VEGF-A) in String db
VGFA stringdb
updated 21 days ago by ▴ 10 • written 3 months ago by ▴ 20
5
votes
13
replies
2.0k
views
Tutorial: Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
R Ubuntu Linux Bioconductor Rstudio
updated 27 days ago by 82k • written 28 days ago by ★ 1.7k
5
votes
2
replies
2.6k
views
How do you evaluate the effectiveness of the batch effect algorithm?
Batch-Effect
updated 29 days ago by 43k • written 9.2 years ago by ▴ 110
5
votes
5
replies
309
views
Error in dimnames(x) <- dn : length of 'dimnames' [2] not equal to array extent
EGSEA
9 days ago by Chris ▴ 280
5
votes
5
replies
665
views
Tutorial: how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix RNAseq R
updated 14 days ago by • 0 • written 22 days ago by ★ 3.9k
5
votes
4
replies
730
views
DEG analysis of RNA-seq data across multiple tissues and two conditions
RNA-seq EdgeR DEGs DESeq2
29 days ago by BioinfGuru ★ 1.7k
5
votes
5
replies
340
views
Problem with data downloaded from Short Reads Archive (SRA)
SRA DADA2 metabarcoding
updated 15 days ago by ▴ 40 • written 15 days ago by ▴ 150
4
votes
5
replies
3.4k
views
How to compare compare two Sam files to check mapping
alignment
updated 9 days ago by ▴ 90 • written 6.4 years ago by ▴ 60
4
votes
6
replies
3.8k
views
How to interpret DEXseq results in therms of significance
DEXseq RNA-Seq exon
updated 11 days ago by ▴ 30 • written 6.7 years ago by ★ 1.2k
4
votes
0
replies
159
views
Herald: The Biostar Herald for Monday, April 29, 2024
herald
18 days ago by Biostar 2.8k
4
votes
8
replies
766
views
Create a new bed file with all pairwise combinations between two other bed files, based on bp distance
SNPs BED eqtl bedtools
updated 20 days ago by 35k • written 21 days ago by ▴ 10
4
votes
2
replies
275
views
GRCh38.gmap file
gnomix gmap
13 days ago by lorena9132 ▴ 10
4
votes
2
replies
3.8k
views
DESeq2 design and batch effect
RNA-Seq batch-effect DESeq2 Salmon
updated 29 days ago by 43k • written 6.6 years ago by ▴ 30
4
votes
6
replies
1.2k
views
Soft-clipping read ends based on read group
ancient molecule at bam DNA RG ends clipping damage
updated 9 days ago by ▴ 10 • written 2.5 years ago by • 0
4
votes
15
replies
1.7k
views
how to test for differential expression in samples where a global increase in gene expression is expected
edgeR DESeq Differential-Expression RNA-Seq
updated 13 days ago by ★ 7.2k • written 5 months ago by ▴ 10
4
votes
2
replies
273
views
How can I analyze normalized expression data?
DEseq2 RNA-seq
8 days ago by mnx0723 • 0
4
votes
9
replies
399
views
Faster Needleman-Wunsch rapid global alignment of two sequences?
Needleman-Wunsch alignment
9 hours ago by Gabriel R. ★ 2.9k
4
votes
9
replies
2.2k
views
6 follow
Same sequencing sample in multiple lanes. How to analyse it?
sequencing bowtie2 alignment samtools ngs
updated 14 days ago by • 0 • written 2.2 years ago by • 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 • 0
4
votes
1
reply
202
views
Extracting only 4-fold degenerate sites from gene sequences/alignments?
alignments
3 days ago by J. ▴ 40
4
votes
6
replies
806
views
7 follow
Heatmap and rna-seq
RNA-Seq Heatmap
updated 20 days ago by ★ 6.0k • written 24 days ago by ▴ 10
4
votes
9
replies
2.1k
views
Legend and hap files for imputation with 38 build
reference 38build impute imputation
18 days ago by anna ▴ 20
4
votes
4
replies
3.0k
views
CNVkit for somatic copy number detection
cnv cnvkit exome WES
updated 3 days ago by • 0 • written 5.1 years ago by • 0
4
votes
3
replies
439
views
Source other conda environments in a nextflow pipeline when nextflow itself is in a conda environment?
hpc conda nextflow
updated 20 days ago by 3.2k • written 21 days ago by ▴ 40
4
votes
2
replies
266
views
Analysis of intronic reads included scRNA-seq data
single-cell
updated 13 days ago by 43k • written 14 days ago by ▴ 40
4
votes
6
replies
3.9k
views
Taking the difference of two VCFs (or removing singletons)
genome sequencing singleton SNP filter
updated 17 days ago by ▴ 20 • written 9.7 years ago by ▴ 40
4
votes
7
replies
412
views
How does gene length effect the number of reads mapped
RNA-seq CPM sequencing
3 days ago by Chen • 0
4
votes
7
replies
437
views
In one PCA plot, can I calculate the percentage of different factors that contribute to the PCA?
PCA R VARIANCE
updated 10 hours ago by ▴ 130 • written 2 days ago by ▴ 20
4
votes
7
replies
605
views
To get p-values for the TPM
P-value TPM RSEM
updated 22 days ago by ★ 6.0k • written 23 days ago by • 0
4
votes
5
replies
453
views
Figures are disappeared from html report of SnpEff
HTML SnpEff
18 days ago by analyst ▴ 50
4
votes
12
replies
4.9k
views
10 follow
How to analyze Infinium Mouse Methylation BeadChip array data?
Methylation Experience Illumina Mouse
updated 8 days ago by ▴ 180 • written 3.0 years ago by ▴ 20
4
votes
7
replies
633
views
Very low RNA splicing rate for pulmonary AT2 cells
RNA-velocity scVelo scRNA-seq splicing
18 days ago by e.r.zakiev ▴ 210
4
votes
1
reply
356
views
How to use limma to find differentially expressed genes in response to a continuous variable
limma voom R
18 days ago by pairedttest ▴ 10
4
votes
5
replies
4.3k
views
Tool: GRIDSS: the Genomic Rearrangement IDentification Software Suite
Assembly Structural-Variation Variant-Calling
updated 23 hours ago by ▴ 520 • written 7.2 years ago by ★ 2.9k
4
votes
2
replies
375
views
Assume "yes" as the answer to any prompts with bioconda
docker container bioconda
updated 29 days ago by 8.6k • written 29 days ago by ▴ 20
4
votes
3
replies
2.9k
views
How to solve the error 'ERROR::MATE_NOT_FOUND:Found xxx unpaired mates' when run SamToFastq
samtofasq picard validatesamfile
updated 8 days ago by 161k • written 8 days ago by ★ 1.2k
4
votes
11
replies
883
views
Redirection of Duplicate PMIDs
pubmed pmid
updated 23 days ago by 4.2k • written 24 days ago by • 0
4
votes
1
reply
257
views
LD-prune variants while maintaining a list of SNPs
snp vcf plink filtering independent
updated 11 days ago by 11k • written 13 days ago by ▴ 560
3
votes
3
replies
375
views
What analysis suitable to identify similarly expressed genes between two samples (treated vs untreated). Contrary to DGE analysis,
Gene-Expression RNA NOISeq DGE
updated 14 days ago by 82k • written 15 days ago by • 0
3
votes
3
replies
368
views
Sequence read length shorter than flow cell specification
illumina NGS sequencing
updated 22 days ago by 14k • written 22 days ago by • 0
3
votes
3
replies
282
views
what is another word for a BLAST "hit"?
blast alignment
7 days ago by dec986 ▴ 380
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
8
replies
600
views
How to access TCGA samples that were treated with a specific drug?
TCGA RNA-seq
11 days ago by Qroid ▴ 40
3
votes
3
replies
3.0k
views
Quick way to Identify batch effect from covariates?
bioconductor batch-effect
updated 29 days ago by 43k • written 7.9 years ago by ★ 3.4k
3
votes
3
replies
268
views
Gene Specific coverage from WGS data
WGS SARS-CoV2
updated 4 days ago by 43k • written 17 days ago by • 0
3
votes
9
replies
616
views
Is it Acceptable to Have Uniform Quality Scores in a FASTQ File?
FASTQ
updated 23 days ago by 100k • written 25 days ago by • 0
3
votes
1
reply
629
views
What is the normalization status of metabric data?
metabric normalization microarray cbioportal
updated 29 days ago by ▴ 20 • written 20 months ago by ★ 4.3k
3
votes
5
replies
636
views
SLURM submission problem: Indexing the Reference Genome is not done in STAR
align RNA-Seq linux STAR
25 days ago by n_navy • 0
3
votes
5
replies
395
views
Converting CRAM to FastQ
GATK samtools cram SamToFastq fastq
14 days ago by Maverick ▴ 10
760 results • Page 2 of 16
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Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
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Comment: Differentially Expressed Genes between two conditions (scRNA, single GEO dataset
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Recent Replies
Answer: Design for complex RNA-Seq experiment using Deseq2 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 LauferVA 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 by ntsopoul ▴ 60
I use Trim Galore which automatically recognizes adaptors. https://github.com/FelixKrueger/TrimGalore Here is the script I am using for…
Answer: Trimming tool by 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: zero TPM for many gene including housekeeping when using kallisto by ashkan ▴ 160
@atpoint I checked all transcripts of GAPDH. they all have 0 TPM.
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 by alanh ▴ 170
For more details about what `samtools quickcheck` actually checks for, add a few `-v`'s to the command line. $ samtools quickcheck -…
Comment: How to handle duplicated genes in TCGA data? by Zhenyu Zhang ★ 1.2k
Second what is said above, ensembl_id is the unique identifier. As a good bioinformatics habit, always use unique identifier for your anal…
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation by hannes.bongartz • 0
It doesn't work. The annotation labels are still in a default fontsize. I cant find a way to set the fontsize.
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation by Ram 43k
Yes. The solution to most things with ComplexHeatmap is to play around with parameters.
Comment: Reconstruction of locus, order contigs by BATMAN • 0
I do not want to re-annotate the genome. I ask if there is a way to extract the region aligned with the mauve, in .gbk format.
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