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122,012 results • Page 604 of 2441
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Demultiplex Quality
sequence demultiplex illumina
updated 4.2 years ago by 154k • written 4.2 years ago by • 0
0
votes
0
replies
542
views
Plink extracting individuals based on certain SNPs
Plink genotypes SNP
updated 4.2 years ago by 45k • written 4.2 years ago by • 0
0
votes
0
replies
740
views
Job: Post-doc Job Opportunity in NYC
post-doc systems-biology computational-biology
updated 2.6 years ago by 45k • written 4.2 years ago by ▴ 30
1
vote
1
reply
1.1k
views
Retrieving Clusters from Clustermatrix, obtained with Hierarchical Clustering
seaborn python Hierarchical clustering
updated 4.2 years ago by ▴ 650 • written 4.2 years ago by ▴ 70
0
votes
0
replies
731
views
Job: Job Opening: Bioinformatician and Sr. Bioinformatician at UCSC's Genomics Institute
genomics
updated 2.6 years ago by 45k • written 4.2 years ago by ▴ 30
6
votes
4
replies
1.7k
views
DESeq2 - design matrix and interaction terms
deseq2 rnaseq interactions LRT
updated 3.5 years ago by ★ 1.3k • written 4.2 years ago by • 0
1
vote
2
replies
2.2k
views
Interpretation of DESeq2 DE-analysis
differential DESeq2 expression R
updated 3.5 years ago by ★ 1.3k • written 4.2 years ago by ▴ 50
0
votes
0
replies
731
views
Kraken2 with phylogeny as input (instead of taxonomy)?
kraken phylogeny
4.2 years ago by cjb ▴ 10
0
votes
0
replies
747
views
Constructing GRNs from multimodal data?
multimodal scRNA-seq SCENIC GRN scATAC-seq
updated 4.2 years ago by 154k • written 4.2 years ago by ▴ 10
4
votes
4
replies
3.7k
views
Cell hashing vs barcoding
barcoding hashing
updated 3.8 years ago by ▴ 40 • written 4.2 years ago by • 0
0
votes
0
replies
1.2k
views
Pybedtools/pyranges/Bedtools: How to Identify features near genes, but where window size is only comprised of host sequence (excluding features)?
bedtools genetics pyranges pybedtools
4.1 years ago by Tobias • 0
3
votes
5
replies
5.2k
views
CRAM to BAM using SAMTOOLS
SAMTOOLS CRAM BAM
updated 4.2 years ago by 166k • written 4.2 years ago by • 0
1
vote
0
replies
589
views
Is there an updated Arabidopsis annotation for Mapman Desktop app?
Mapman Arabidopsis anotaions Updated
4.2 years ago by finn.scout.claassens ▴ 10
2
votes
2
replies
1.1k
views
How to map a file with mulitple olisogos to a reference genome
blastn
4.2 years ago by dominik.lagler ▴ 30
4
votes
3
replies
1.7k
views
Finding metagenomic short read sequences
antimicrobial reference short sequences reads data metagenomic resistance
updated 4.2 years ago by ★ 1.1k • written 4.2 years ago by ▴ 100
0
votes
0
replies
1.1k
views
Job: Group Leader – Structural Systems Biology
Computational-Systems-Biology
updated 2.8 years ago by 45k • written 4.2 years ago by ▴ 30
0
votes
0
replies
581
views
DE analysis for single cell data with strong batch effect or different sequencing depth
cell expression differential de single
4.2 years ago by Cheng Wei • 0
1
vote
2
replies
979
views
vcf file genotypes
genotype vcftools GATK
4.2 years ago by Vic ▴ 140
0
votes
0
replies
2.2k
views
Making box plot with pvalue for a set of genes across clusters or condition using seurat RNA slot count data
seurat boxplot scrna
4.2 years ago by sam ▴ 30
4
votes
3
replies
2.1k
views
Decoy sequence for human reference GRCh38 assembly
reference genome Decoy assembly Human
updated 4.2 years ago by ★ 1.1k • written 4.2 years ago by ▴ 70
0
votes
0
replies
479
views
Selecting a group of genes for coexpression network
gene_coexpression_network rnaseq
4.2 years ago by GenesisBio • 0
0
votes
2
replies
1.3k
views
Gene filtering based on Coefficient of Variation > 50%
microarray
4.2 years ago by smrutimayipanda ▴ 20
0
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4
replies
2.2k
views
Best practice for running GATK VQSR on X chromosome
WGS GATK WES
3.9 years ago by samuelandjw ▴ 270
1
vote
1
reply
892
views
How to perform differential expression analysis without the matched normal tissue data?
RNA-Seq Differential Expression DE ICGC PCAWG
updated 4.2 years ago by 89k • written 4.2 years ago by ▴ 110
8
votes
7
replies
11k
views
8 follow
How to get rs number for the variants list?
SNP
updated 4.2 years ago by ▴ 40 • written 8.7 years ago by ▴ 10
22
votes
8
replies
16k
views
6 follow
SNP rsid by location?
snp
updated 4.2 years ago by ▴ 40 • written 12.7 years ago by ▴ 350
2
votes
2
replies
2.4k
views
Change STAR Parameters in rsem-calculate-expression
RNA-Seq RSEM STAR
updated 4.2 years ago by 23k • written 4.2 years ago by ▴ 340
3
votes
2
replies
1.7k
views
Percentages in relative abundance of 16s rRNA gene
metagenomics arn abundance relative 16s
updated 4.2 years ago by ▴ 590 • written 4.2 years ago by • 0
0
votes
2
replies
1.3k
views
Jupyterlab / Python : OSError and MemoryError help
Jupyterlab GSEApy GSEA Python
updated 4.2 years ago by 154k • written 4.2 years ago by ▴ 160
0
votes
2
replies
990
views
Testing the net differences between 2 treatments, over the control
T-test
4.2 years ago by haasroni • 0
0
votes
3
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3.8k
views
Seurt Rename Orig.ident
Seurta cell RNAseq Single
updated 4.2 years ago by 89k • written 4.2 years ago by • 0
0
votes
0
replies
576
views
Interpreting Bedtools Intersection Between BAM and BED Files
bedtools
4.2 years ago by Steven Mick • 0
0
votes
3
replies
3.6k
views
How to calculate genotype concordance, comparing two .vcf files with Picard or SnpSift
picard GenotypeConcordance SnpSift
updated 4.2 years ago by 166k • written 5.1 years ago by ▴ 220
2
votes
3
replies
1.8k
views
Forum: Freelancers for bioinformatics web development
bioinformatics web-development freelance
updated 4.2 years ago by ★ 2.9k • written 4.2 years ago by ▴ 20
1
vote
2
replies
2.2k
views
Where can I find GPL571 cdf file?
CDF file Partek Gene Expression Value
updated 4.2 years ago by • 0 • written 7.7 years ago by ▴ 10
1
vote
0
replies
595
views
Exonerate edit distance threshold
Exonerate
updated 4.2 years ago by 11k • written 4.2 years ago by • 0
3
votes
1
reply
5.2k
views
Tutorial: Affymetrix HTA 2.0 id conversion
biomart HTA affymetrix Affymetrix 2.0
updated 20 months ago by ▴ 120 • written 4.2 years ago by 89k
2
votes
1
reply
1.1k
views
Python modules/code to generate triangulations of Solvent Excluded Surfaces
Proteins Visualization Python Molecular
4.2 years ago by Tzunami ▴ 10
0
votes
0
replies
794
views
Add SM group STAR
samtools variant RNA-seq calling GATK STAR
4.2 years ago by Lucy ▴ 170
3
votes
4
replies
1.3k
views
Sam file arrangement
BAM BED
updated 4.2 years ago by 89k • written 4.2 years ago by • 0
1
vote
1
reply
1.0k
views
Syntax error when running ScaleHD
repeats expansion illumina ScaleHD amplicon
updated 3.2 years ago by ▴ 60 • written 4.2 years ago by ▴ 210
2
votes
4
replies
2.7k
views
interpreting heatmap on metascape
metascape heatmap annotation
updated 2.7 years ago by 45k • written 4.2 years ago by • 0
0
votes
3
replies
1.3k
views
Methylome Data or DE Analysis
DE DESEQ2 Methylome
updated 4.2 years ago by 89k • written 4.2 years ago by ▴ 10
2
votes
13
replies
3.2k
views
gene expression of specifics gene
RNA-Seq
4.2 years ago by Bioinformatics1 ▴ 10
0
votes
6
replies
2.3k
views
how to create heat map using ggplot2 in R?
R
updated 4.2 years ago by 89k • written 4.2 years ago by • 0
2
votes
2
replies
1.2k
views
Can Exonerate return only the Cigar string?
Exonerate
updated 4.2 years ago by 45k • written 4.2 years ago by • 0
0
votes
3
replies
1.8k
views
What kinds of GSEA would be most appropriate for RNA-Seq Data?
rnaseq R
updated 4.2 years ago by 3.3k • written 4.2 years ago by ▴ 20
4
votes
6
replies
7.6k
views
Annotation Affymetrix probesets to Gene symbols
RNA-Seq R affymetrix gene
updated 4.2 years ago by 89k • written 6.0 years ago by ▴ 130
3
votes
8
replies
5.6k
views
WGCNA adjust p value
statistics WGCNA
updated 13 months ago by • 0 • written 4.2 years ago by ▴ 10
0
votes
5
replies
2.0k
views
Removing specified range of bases from middle of the contigs and creating new sequences
Contigs Assembly fastafile
updated 4.2 years ago by 21k • written 4.2 years ago by ▴ 280
122,012 results • Page 604 of 2441
Recent Votes
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?
Answer: Scaling RNA-Seq data before clustering?
Online course: RNA sequencing data analysis using R and Bioconductor - 3–14 November
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Recent Replies
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.
Comment: DESeq2 on metagenome KO counts by ATpoint 89k
This statement makes zero sense in response to what I wrote.
Comment: DESeq2 on metagenome KO counts by Aleksandra ▴ 190
I focused on the fact that DESeq2 models overdispersion, but overlooked its implicit assumption: normalisation works when the main source o…
Comment: DESeq2 on metagenome KO counts by Aleksandra ▴ 190
Thank you very much. I mistakenly drew a superficial analogy. I equated KO counters with gene counters.
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