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122,013 results • Page 601 of 2441
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1
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3
replies
2.7k
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formatting error: Calculate LD matrix from bgen file
plink ld_matrix
updated 15 months ago by 45k • written 4.2 years ago by ▴ 160
0
votes
0
replies
724
views
Mixed model analysis using lme4
mixed-model fixed-effect lme4 random-effect lmer
updated 13 months ago by 45k • written 4.2 years ago by ▴ 20
12
votes
8
replies
4.5k
views
7 follow
Highly used R packages with no Python equivalent
package python r software
updated 4.2 years ago by 11k • written 4.2 years ago by • 0
1
vote
2
replies
3.7k
views
install ensembl-vep
ensembl-vep install
4.2 years ago by yueli7 ▴ 250
2
votes
3
replies
1.4k
views
How to separate sub-families from transposons sequence based fasta files?
fasta transposons
updated 2.6 years ago by 45k • written 4.2 years ago by • 0
2
votes
1
reply
1.1k
views
calculating fold change from dataframe
fold frame change data
updated 4.2 years ago by 89k • written 4.2 years ago by • 0
1
vote
4
replies
1.4k
views
Variant calling from 5 MB regions coming from contrasting cultivars
calling alignment variant
4.2 years ago by VenGeno ▴ 100
0
votes
0
replies
564
views
variant filtration with gene names or position
variant-filtration
4.2 years ago by ziziqolo ▴ 10
0
votes
1
reply
871
views
How does find the sequence of each oligonucleotide in microarray probe?
Affymetrics technology probe microarray
updated 4.2 years ago by 21k • written 4.2 years ago by ▴ 170
2
votes
3
replies
2.8k
views
How to subset vcf by sample and write?
bcftools vcf
updated 4.2 years ago by ▴ 480 • written 4.2 years ago by ▴ 50
0
votes
4
replies
2.4k
views
Can RNA-Seq be used for TMB calculation?
RNA-Seq tmb
updated 4.2 years ago by 89k • written 4.9 years ago by ▴ 10
0
votes
5
replies
8.6k
views
bcftools consensus still returns "Could not parse the header" error
bcftools samtools
4.2 years ago by shpak.max ▴ 60
1
vote
1
reply
1.7k
views
Detecting and masking repeats with EDTA: Low threshold vs complete masking
repeat masker. annotation genome EDTA
updated 4.2 years ago by ▴ 30 • written 4.3 years ago by • 0
7
votes
5
replies
1.7k
views
Why does Txdb transcript length not always match to transcript end-start position?
biomart transcript Txdb length transcription
updated 4.2 years ago by 22k • written 4.2 years ago by ▴ 20
0
votes
5
replies
3.0k
views
printing volcano plot
bioinfokit python gene_expression volcano_plot
updated 4.2 years ago by 45k • written 4.2 years ago by • 0
1
vote
0
replies
516
views
Myeloma Data Search
myeloma
updated 2.8 years ago by 45k • written 4.2 years ago by ▴ 140
2
votes
4
replies
5.6k
views
Interpreting bcftools isec output
bcftools isec intersection vcf
updated 3.8 years ago by 45k • written 4.2 years ago by ▴ 30
5
votes
4
replies
3.1k
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 18 months ago by 45k • written 4.2 years ago by ▴ 180
0
votes
0
replies
975
views
Job: Product Manager for Online Bioinformatics Resources for Online Bioinformatics Resources
Resources Product-Manager
updated 2.6 years ago by 45k • written 4.2 years ago by ▴ 90
0
votes
2
replies
2.4k
views
[pysam] How to find both both primary and supplementary read？
NGS pysam bam python SAM
4.2 years ago by octpus616 ▴ 120
1
vote
2
replies
1.5k
views
question about Mutation Annotation Format (MAF) variant classifications
annotation ICGC MAF R
4.2 years ago by Charles Murtaugh ▴ 50
0
votes
1
reply
788
views
Cytogenetics Database
database ISCN Cytogenetics
4.2 years ago by Jng • 0
0
votes
3
replies
1.6k
views
KCCG /ClinSV issue with hg38
variation human genome wgs
4.2 years ago by Ishak ▴ 20
13
votes
15
replies
13k
views
6 follow
Where To Find Annotation File For Agilent Microarray?
annotation
updated 4.2 years ago by ▴ 20 • written 12.2 years ago by ★ 1.1k
0
votes
0
replies
651
views
Find causal mutation for a special trait in one population
Detecting SV SNP
4.2 years ago by dominik.lagler ▴ 30
0
votes
0
replies
722
views
Genbank submission problem
tbl genbank gbff submission
4.2 years ago by hs • 0
0
votes
1
reply
1.2k
views
errors installing HTSeq
HTSeq RNAseq
updated 4.2 years ago by 154k • written 4.2 years ago by • 0
2
votes
3
replies
1.2k
views
Genotyping variants from BAM (human)
genotyping
updated 4.2 years ago by 154k • written 4.2 years ago by ★ 3.0k
0
votes
0
replies
579
views
Getting the average of pdb structure from only one trajectory
PBD Trajectory
updated 4.2 years ago by 56k • written 4.2 years ago by • 0
3
votes
1
reply
4.1k
views
Issues with enricher() function from clusterProfiler
clusterProfiler enrichment
updated 4.2 years ago by ★ 2.6k • written 4.7 years ago by ▴ 10
0
votes
13
replies
3.5k
views
Default CNV call thresholds for haplotype chromosome s
haplotype cnvkit mal calling cnv
updated 4.2 years ago by ★ 3.0k • written 4.2 years ago by ▴ 40
0
votes
0
replies
922
views
Job: PostDoc in Bioinformatics / Machine Learning (Luxembourg, Europe)
PostDoc machine-learning
updated 2.6 years ago by 45k • written 4.2 years ago by ▴ 130
4
votes
4
replies
2.8k
views
How do I export a KaryoploteR plot or insert it into a grid/lattice? Can I assign a KaryoploteR plot to a variable?
karyoploteR grid ideograms
updated 4.2 years ago by ▴ 120 • written 4.2 years ago by ▴ 20
2
votes
3
replies
1.7k
views
Cannot compile Lumpy-SV.
structural KCCG ClinSV variation
4.2 years ago by Ishak ▴ 20
6
votes
5
replies
1.9k
views
How to Append numbers on ALL headers in FASTA (e.g., >gene#1)?
FASTA perl Python
updated 4.2 years ago by 21k • written 4.2 years ago by ▴ 10
0
votes
2
replies
1.5k
views
How do you perform in silico PCR ?
taxonomy PCR NCBI
updated 4.2 years ago by ▴ 840 • written 4.2 years ago by • 0
4
votes
2
replies
2.5k
views
convert GenBank formatted sequence file to FASTA format
fasta python genback
updated 4.2 years ago by 45k • written 4.2 years ago by ▴ 20
6
votes
6
replies
5.6k
views
SRA-tools fasterq-dump and cellranger issues
cellranger
updated 3.0 years ago by ▴ 20 • written 4.2 years ago by ▴ 10
0
votes
4
replies
1.8k
views
Functional enrichment and visualization of metatranscriptomics data
clusterProfiler
4.2 years ago by shail.nair05 ▴ 20
1
vote
0
replies
668
views
question about integrating snRNA seq data from different batch and different experimental conditions
Seurat batch integrate
4.2 years ago by Wonjae ▴ 10
0
votes
0
replies
1.2k
views
Job: Bioinformatics Postdoctoral Research Associate
postdoc multi-omics Python Matlab
updated 2.6 years ago by 45k • written 4.2 years ago by • 0
0
votes
1
reply
1.4k
views
Popgenome nvalid sites
vcf Popgenome
4.2 years ago by shinken123 ▴ 150
3
votes
2
replies
1.4k
views
How to perform DESEQ2 analysis when there are three treatments (one of them being a reference)?
comparisons DESEQ2 expression multiple differential analysis
4.2 years ago by mrj ▴ 180
0
votes
6
replies
3.5k
views
fgsea result "size" parameter - can I pull out size of the original pathway?
GSEA fgsea pathway R
updated 4.2 years ago by ★ 1.0k • written 4.2 years ago by ▴ 20
0
votes
2
replies
1.5k
views
[Biopython] endweight, endopen and endextend equivalent for Bio.Align.PairwiseAligner()
alignment Needle Biopython
4.2 years ago by gaspanic987 • 0
4
votes
1
reply
1.8k
views
Ensembl Homology: Human orthologs of mouse genes labled "many2many" but correspond to a single mouse ortholog
homology Ensembl
updated 4.2 years ago by ▴ 270 • written 4.4 years ago by ▴ 110
2
votes
12
replies
7.2k
views
Trying to read multiple CSV files in a folder and add filename to each column in R
R Merging
4.2 years ago by mxz707 • 0
0
votes
1
reply
959
views
How to sum/merge two hicpro raw matrices in python/r
matrices hic
updated 4.2 years ago by 21k • written 4.2 years ago by • 0
0
votes
0
replies
566
views
analyzing copy number variation in sunflower with cn.mops
cn.mops copy.number.variation
4.2 years ago by ziv_attia • 0
3
votes
1
reply
3.2k
views
Mitochondrial percentage in Seurat
Seurat R
updated 3.6 years ago by ▴ 940 • written 4.2 years ago by ★ 4.4k
122,013 results • Page 601 of 2441
Recent Votes
Answer: 1 vs 1 DEG analysis in scrna seq data
Comment: installation of package ‘DESeq2’ had non-zero exit status
Answer: Recommendations for 200 SNP markers genotyping
Comment: Reasonable number of SNPs in a bacterial genome.
The Biostar Handbook. A bioinformatics e-book for beginners.
Genome Assembly QC from BAM files
Answer: Scaling RNA-Seq data before clustering?
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Recent Replies
Answer: 1 vs 1 DEG analysis in scrna seq data by ATpoint 89k
The only option you have is to treat every single cell as a replicate. That has the obvious downside that any effect can be a donor-unique …
Answer: GUI commercial software for 10x single cell gene expression analysis by firestar ★ 1.7k
An open-source option: [kana](https://www.kanaverse.org/kana/).
Comment: Brave: Bioinformatics Reactive Analysis and Visualization Engine by Edward • 0
Yes, we plan to make English the primary language of the Brave UI.
Comment: Reasonable number of SNPs in a bacterial genome. by michael.ante ★ 4.0k
If your bacterial species is a (human) pathogen, you might want to check outbreak analysis papers of that species. In general, you find t…
Comment: hisat2 error-Paired end reads not equal or lack of RAM/disk space? by lieven.sterck 16k
ok, missed that ... in any case that should not happen indeed. How did you determine that the files are not equal? I can indeed also see t…
Comment: Brave: Bioinformatics Reactive Analysis and Visualization Engine by Ram 45k
Do you have a plan to make an English version of the UI?
Comment: Brave: Bioinformatics Reactive Analysis and Visualization Engine by Edward • 0
This can visualize the parameters of the generated workflow, software, and scripts, and manage the docker process of the script, software, …
Comment: Brave: Bioinformatics Reactive Analysis and Visualization Engine by ATpoint 89k
Can you summarize in one sentence what the use case is? Is this a workflow manager?
Comment: Pseudogene - scarce info by ATpoint 89k
This reminds me strongly on my "masters" courses (doesn't deserve that name tbf). "Here is some poorly-described project with little to no …
Answer: scVI vs Harmony, which is better for cell type based clustering in brain tissue? by ATpoint 89k
There is no "better" is my experience. It always depends on the dataset. Try both and integrate your biological knowledge to decide which m…
Comment: DESeq2 on metagenome KO counts by Aleksandra ▴ 190
I just wrote that I misunderstood your initial question.
Comment: DESeq2 on metagenome KO counts by Aleksandra ▴ 190
What exactly did I not get?
Comment: Interpreting genomic features distribution for CUT&RUN peaks by rfran010 ★ 1.7k
If I understand correctly, you see increased signal at TSS sites compared to control (taller peaks in browser). However, 92% of the 450 siS…
Comment: combine VCF from diploid reference/haplotypes for the same sample by cmdcolin ★ 4.3k
this question is a little similar to your previous question (https://www.biostars.org/p/9614638/). just as added info, here is a tool calle…
Comment: hisat2 error-Paired end reads not equal or lack of RAM/disk space? by aj123 ▴ 130
As mentioned above, I just got the raw fastq files from the ftp site listed.
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