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122,010 results • Page 284 of 2441
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2
votes
6
replies
2.4k
views
Bad quality fastq files for analysis
quality bad DNA-seq fastq alignment
2.6 years ago by Gene_MMP8 ▴ 240
1
vote
2
replies
1.1k
views
Handling single-sample VCF after haplotypecaller
VCF
2.6 years ago by Y.H.P • 0
0
votes
0
replies
614
views
MethylR on bam files Gives Error
MethylR bismark
2.6 years ago by anasjamshed ▴ 140
0
votes
1
reply
741
views
pyscenic
pyscenic scenic
2.6 years ago by Andy ▴ 120
3
votes
2
replies
1.2k
views
Human Population Reference Genomes (+Neanderthal?)
comparative-genomics
updated 2.6 years ago by 45k • written 2.6 years ago by • 0
1
vote
1
reply
927
views
just one plot appears in the shiny application not all
plot source shiny code
updated 2.6 years ago by ▴ 370 • written 2.6 years ago by ▴ 80
0
votes
0
replies
681
views
Downsample process in ActiveRegion determination (HaplotypeCaller and Mutect2)
Downsample Mutect2 HaplotypeCaller
2.6 years ago by yxwucq • 0
1
vote
0
replies
1.1k
views
Tool: BioLabDNA - Mac program for DNA analysis and cloning.
cloning DNA protein alignment assembly
2.6 years ago by vytarasov ▴ 180
0
votes
1
reply
1.1k
views
ChrX allele frequency in males and females
A
updated 2.6 years ago by 23k • written 2.6 years ago by ▴ 10
4
votes
5
replies
2.4k
views
colouring variables in r
R
updated 2.6 years ago by 11k • written 2.6 years ago by ▴ 30
2
votes
2
replies
1.1k
views
Nextflow Stringtie: command not found Error
nextflow rna-seq stringtie
updated 2.6 years ago by 89k • written 2.6 years ago by • 0
1
vote
1
reply
840
views
Why is protein folding considered so expensive?
protein-folding
updated 2.6 years ago by ★ 30k • written 2.6 years ago by • 0
13
votes
8
replies
5.8k
views
How to perform synteny alignments and plots only with a gene?
Comparative Evolution Alignment Synteny Genomics
2.6 years ago by Rafael Soler ★ 1.3k
1
vote
1
reply
924
views
Methylation data analysis
methylation
updated 2.6 years ago by 2.9k • written 2.6 years ago by • 0
0
votes
0
replies
909
views
Simes method
simes method SNP R
2.6 years ago by Eliza ▴ 40
0
votes
1
reply
914
views
Distinguishing specific reads from non-specific ones in KIR gene sequencing data
specificity alignment
updated 2.6 years ago by ★ 4.7k • written 2.6 years ago by • 0
10
votes
9
replies
9.1k
views
6 follow
featureCounts Output "The reads are assigned on the single-end mode"
featureCounts alignment counts RNA-seq
updated 10 months ago by ▴ 10 • written 2.6 years ago by ▴ 30
7
votes
6
replies
3.2k
views
Nextflow: No space left on device, process using output directory as input?
nextflow
updated 2.6 years ago by ▴ 410 • written 2.6 years ago by ▴ 350
0
votes
1
reply
707
views
Conformational antigens
Immunoinformatics
updated 2.6 years ago by 45k • written 2.6 years ago by • 0
0
votes
2
replies
1.5k
views
News: Course - Metagenomics, metatranscriptomics, and multi'omics for microbial community Studies
Metagenomics Metatranscriptomics Multiomics
updated 2.6 years ago by 45k • written 2.6 years ago by ★ 2.6k
0
votes
2
replies
1.2k
views
best practice to choose AF threshold based on population number
VCF AF allele-frequency
2.6 years ago by prasundutta87 ▴ 730
2
votes
5
replies
2.5k
views
msigdbr returns the same genesets for mouse as in for human,
msigdbr
updated 2.6 years ago by 13k • written 2.6 years ago by ▴ 260
2
votes
8
replies
2.5k
views
Use bismark files to run methylKit
bismark R
2.6 years ago by anasjamshed ▴ 140
0
votes
0
replies
664
views
selection of 2 by 2 Chi-square Test
statistics Chi-square
updated 2.6 years ago by 45k • written 2.6 years ago by ▴ 20
0
votes
0
replies
666
views
Check most expressed isoform of mouse gene in specific tissue
FANTOM gene-expression MGI mouse
updated 2.6 years ago by 45k • written 2.6 years ago by ▴ 10
1
vote
4
replies
1.5k
views
SRA Data Download
SRA
updated 2.6 years ago by ★ 4.7k • written 2.6 years ago by • 0
5
votes
1
reply
1000
views
How do I retrieve withdrawn or replaced gene id for homosapiens from ncbi gene ?
NCBI Eutils
updated 2.6 years ago by 45k • written 2.6 years ago by ★ 4.4k
2
votes
4
replies
2.7k
views
Benjamini–Hochberg correction, FDR in genes' expressions
False-discovery-rate
updated 2.6 years ago by ★ 4.7k • written 2.6 years ago by • 0
1
vote
0
replies
753
views
gseKEGG with streptomyces coelicolor - No gene can be mapped
streptomyces KEGG clusterProfiler
2.6 years ago by r.evans2 ▴ 10
0
votes
0
replies
1.3k
views
Job: Bioinformatician IRCCS Regina Elena National Cancer Institute, Italy
unix-administration genomics
updated 2.6 years ago by 45k • written 2.6 years ago by • 0
0
votes
0
replies
817
views
Power calculations for the detection of differentially expressed genes in pseudobulk scRNA-seq data
scRNA-seq pseudobulk power RNA-seq
updated 2.6 years ago by 45k • written 2.6 years ago by • 0
2
votes
8
replies
2.4k
views
Depth of Coverage in Mitochondrial Genome with Samtools
samtools depth-of-coverage Mitochondrial-genome
2.6 years ago by Lida • 0
0
votes
1
reply
1.0k
views
Genes near SNP within certain window frame and distance
bedops bedtools
updated 2.6 years ago by 45k • written 2.6 years ago by ▴ 160
0
votes
2
replies
1.5k
views
Very high coverage Nanopore alignment Hg38
IGV nanopore alignment
updated 2.6 years ago by ▴ 730 • written 2.6 years ago by ▴ 350
4
votes
2
replies
1.0k
views
align reads to a custom reference genome
reference_genome custom
updated 2.6 years ago by 8.0k • written 2.6 years ago by • 0
0
votes
0
replies
590
views
95% CI for AUC in R
AUC R
2.6 years ago by dhananya • 0
6
votes
5
replies
4.9k
views
Differential expression analysis tool for single cell RNA-seq data
single-cell RNA-seq DE analysis RNA-Seq
updated 2.6 years ago by ▴ 130 • written 8.0 years ago by ▴ 90
0
votes
1
reply
2.0k
views
comparison between STARsolo and cellranger
STARsolo cellranger
2.5 years ago by dalibenam64 • 0
3
votes
3
replies
2.9k
views
bcl-convert demux of flowcell with mixed index lengths
demultiplexing bcl-convert demux illumina sequencing
2.6 years ago by rustykb ▴ 20
0
votes
6
replies
4.2k
views
RepeatMasker species error
species repeatmasker
updated 2.6 years ago by • 0 • written 4.0 years ago by • 0
0
votes
3
replies
1.1k
views
enriched genes PPI network
string
2.6 years ago by yueli7 ▴ 250
7
votes
9
replies
7.6k
views
Downloading NCBI Blast nt database
nucleotide blast nt genomics database
updated 2.6 years ago by ▴ 120 • written 2.6 years ago by ▴ 10
0
votes
1
reply
781
views
building model with lectin array data and patient data
lectin model
updated 2.6 years ago by 89k • written 2.6 years ago by • 0
2
votes
3
replies
1.8k
views
How to create a fasta file from a list of sequences
fasta sequences DNA
updated 2.6 years ago by ▴ 120 • written 2.6 years ago by ▴ 20
0
votes
4
replies
2.2k
views
how to separate a column to some different columns in R
R
updated 2.6 years ago by 12k • written 2.6 years ago by • 0
0
votes
0
replies
660
views
How to find association between a gene-rsid and AD
association Loci LD AD
2.6 years ago by rheab1230 ▴ 150
0
votes
2
replies
923
views
Finding repeats in dna sequences
OP
2.6 years ago by ojaswinipandey • 0
1
vote
3
replies
1.2k
views
Genetic Carrier Screening Test
ANNOVAR Mappin VEP Maverick
updated 2.6 years ago by 5.1k • written 2.6 years ago by • 0
0
votes
5
replies
1.9k
views
How to get human cDNA sequences together with UTR regions?
transcripts cDNA genome rna-seq
updated 2.6 years ago by 103k • written 2.6 years ago by ▴ 320
0
votes
0
replies
746
views
Why DEG analysis of the same region in two different datasets results in different sets of DEGs?
single integration cell DEG design analysis
2.6 years ago by paria ▴ 110
122,010 results • Page 284 of 2441
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Comment: GUI commercial software for 10x single cell gene expression analysis
Manual Genome Curation using PretextView course
Answer: How to get proteins from GFF file resulted from MAKER annotation
Comment: DESeq2 on metagenome KO counts
Answer: DESeq2 on metagenome KO counts
Answer: DESeq2 on metagenome KO counts
Comment: GUI commercial software for 10x single cell gene expression analysis
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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 ▴ 180
I just wrote that I misunderstood your initial question.
Comment: DESeq2 on metagenome KO counts by Aleksandra ▴ 180
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 ▴ 180
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 ▴ 180
Thank you very much. I mistakenly drew a superficial analogy. I equated KO counters with gene counters.
Comment: DESeq2 on metagenome KO counts by ATpoint 89k
Both vst or logcpm will favor expression level (magnitude of counts) rather than differences in a hclust/heatmap. For differences you need …
Comment: DESeq2 on metagenome KO counts by ATpoint 89k
The DESeq2 developer has advised many times against DESeq2 for metagenomics. Please search for related posts over at support.bioconductor.o…
Answer: DESeq2 on metagenome KO counts by andres.firrincieli 3.9k
I wouldn’t use DESeq2 on aggregated raw counts per KO, because doing so means accepting two pretty big assumptions: 1. All genes with t…
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