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Plink: Number of Samples reducing after merging multiple bed,bim,fam files with Plink's --merge-list function
--merge-list fam_file Plink
4.4 years ago by Swetaleena • 0
1
vote
2
replies
1.3k
views
single cell RNA QC
scRNA QC
4.4 years ago by leranwangcs ▴ 150
0
votes
0
replies
1.2k
views
Need to extract specific VCF sample IDs from 1000Genomes project in the group 30x 1000 genomes genotypes aligned to gr38
1000genomes extraction vcf data
4.4 years ago by screadore ▴ 20
1
vote
6
replies
1.9k
views
Next Generation Sequencing: in which sequencing technology the read can Not exceed the fragment length?
NGS Nanopore Illumina Pacbio
updated 4.4 years ago by 15k • written 4.4 years ago by ▴ 20
1
vote
1
reply
891
views
How to identify first codon (Methionine) misssense variants?
Mutation ANNOVAR Missense
updated 4.4 years ago by 166k • written 4.4 years ago by ▴ 50
2
votes
2
replies
1.1k
views
Forum: What is your experience with the customer support of Oxford University Press?
oup
updated 4.4 years ago by 89k • written 4.4 years ago by ▴ 20
0
votes
1
reply
1.2k
views
How to solve Warning: [blastx] Taxonomy name
alignment blastx warning blast
updated 4.4 years ago by 153k • written 4.4 years ago by ▴ 760
7
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3
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2.7k
views
News: New NCBI Datasets home and documentation pages provide easier access
ncbi gene SARS-CoV-2 genome
updated 4.4 years ago by 103k • written 4.4 years ago by ▴ 50
5
votes
3
replies
2.4k
views
Identification of modules of genes that vary over pseudotime (scRNA-seq pseudotime analysis)
modules scRNA-seq singlecell pseudotime RNA-seq
updated 4.4 years ago by ★ 19k • written 4.4 years ago by ▴ 170
1
vote
1
reply
636
views
How align identical sequence from two dataframe in a new dataframe ?
alignment Rstudio aminoacid Identical sequence
updated 4.4 years ago by 89k • written 4.4 years ago by • 0
0
votes
0
replies
992
views
What is "rl" in SAM format
SAM format
4.4 years ago by ymat • 0
0
votes
1
reply
4.1k
views
How to increase the size of the top annotation bars in Complexheatmap
plot annotation ComplexHeatmap heatmap
4.4 years ago by mohammedtoufiq91 ▴ 270
0
votes
2
replies
1.8k
views
How to produce overlapping QQ-plot from GWAS results?
R data-visalization GWAS SNP
4.4 years ago by anikcropscience ▴ 270
1
vote
8
replies
5.0k
views
XGBoost on the unbalanced data
unbalanced_data
4.4 years ago by mrashad ▴ 80
5
votes
5
replies
3.4k
views
How to remove all-N sequence entries from fasta file.
awk perl
updated 4.4 years ago by 21k • written 4.4 years ago by ▴ 30
0
votes
1
reply
592
views
Inserting N bases at 5' end of clipped reads
GenomicAlignments Samtools cutadapt Bowtie2
updated 4.4 years ago by 166k • written 4.4 years ago by • 0
2
votes
6
replies
4.0k
views
for loop to filter dataframe based on conditions
r loop filter
4.4 years ago by katinstack • 0
0
votes
0
replies
819
views
Plink2: Determine if allele2 is major or ref
plink2 plink
4.4 years ago by Brynjar ▴ 20
0
votes
0
replies
651
views
How to correctly map CORALL-generated RNA-seq data to a reference genome?
CORALL stranded mapping paired-end RNA-seq
4.4 years ago by niklasjoshua.ebner • 0
3
votes
7
replies
2.7k
views
Can too high of a ChIPQC RiP% be indicative of insufficient stringency in peak calling?
R ChIP-seq ChIPQC
updated 4.4 years ago by 15k • written 4.4 years ago by ▴ 30
2
votes
1
reply
1.5k
views
RPKM and FPKM quality control check and filtration
scRNA-Seq
updated 4.4 years ago by 6.5k • written 4.4 years ago by • 0
1
vote
3
replies
1.7k
views
Lower bound of y-axis hidden in UpSet plot in R, how to avoid this
Plot R UpSet
updated 4.4 years ago by 89k • written 4.4 years ago by • 0
0
votes
3
replies
3.5k
views
No GO-term and no ontology in goseq() output! What am I doing wrong?
goseq GO-term ontology test.cats
updated 3.6 years ago by 45k • written 10.9 years ago by ★ 1.6k
0
votes
2
replies
1.3k
views
Protein Ligand Docking Software Suggestion
Docking software
4.4 years ago by Qinqing • 0
0
votes
3
replies
2.6k
views
beagle error: genotype is missing allele separator
imputation genomics
updated 4.2 years ago by 45k • written 4.4 years ago by • 0
15
votes
15
replies
13k
views
Single cell RNA-seq: how many PCs to use for t-SNE/UMAP?
umap pca scRNA-seq t-sne RNA-seq
4.4 years ago by MutationalMeltdown ▴ 200
1
vote
2
replies
1.6k
views
Mapping EntrezId to Ensembl IDs returns NA for pseudogenes and snoRNA
RNAseq AnnotationDbi
updated 4.4 years ago by ▴ 390 • written 4.4 years ago by • 0
1
vote
5
replies
2.0k
views
Blastn in galaxy
Blastn galaxy
updated 17 months ago by 45k • written 4.4 years ago by • 0
6
votes
12
replies
5.2k
views
7 follow
Multiqc raises the "cannot import name 'gcd' from 'fractions'" error
multiqc linux rna-sq
updated 4.4 years ago by ★ 1.5k • written 4.4 years ago by • 0
0
votes
5
replies
1.6k
views
How to filter reads only with single SNV
filtering_reads SNV amplicon_sequencing SNP
updated 4.4 years ago by 153k • written 4.4 years ago by • 0
0
votes
4
replies
1.5k
views
Bioinformatics researcher looking for an answer on edgeR and DESeq2
rna-seq R edgeR gene
updated 4.4 years ago by 7.6k • written 4.5 years ago by • 0
3
votes
0
replies
955
views
Using bulk RNA-seq deconvolution as covariates in bulk RNA-seq differential expression analysis
cibersort dwls deconvolution
4.4 years ago by telroyjatter ▴ 240
0
votes
0
replies
963
views
How to produce multiple sequence alignment figures with phenotypic data?
alignment multiple-alignment sequence
4.4 years ago by anikcropscience ▴ 270
4
votes
5
replies
2.1k
views
6 follow
Looking for a Whole Genome Sequencing GrCH38 Control group of roughly 250 samples
wgs control whole
updated 4.4 years ago by 2.9k • written 4.4 years ago by ▴ 20
0
votes
1
reply
2.5k
views
how to run and use the ENCODE ATAC-seq pipline
ATAC-seq ENCODE peak
updated 4.4 years ago by 23k • written 4.5 years ago by ▴ 40
4
votes
4
replies
1.9k
views
htseq-count Error '_StepVector_Iterator_obj' object has no attribute 'next'
htseq-count
updated 3.8 years ago by • 0 • written 4.4 years ago by ▴ 20
1
vote
1
reply
1.2k
views
Rare cell population in single cell ATAC-Seq
atac-seq atac
updated 4.4 years ago by ▴ 110 • written 4.4 years ago by ▴ 800
0
votes
1
reply
1.5k
views
How to get GSE data into IGV
ChIP-Seq IGV GSE
updated 4.4 years ago by ▴ 110 • written 4.4 years ago by • 0
0
votes
8
replies
2.3k
views
Split fasta based on symbol and numeric position in header
python fasta sequence genome split
4.4 years ago by Nick Scales • 0
0
votes
0
replies
751
views
Detecting mono-allelic expression in RNA-seq in human
binomial allele_specific gene_expression rna-seq
4.4 years ago by heskett ▴ 110
4
votes
4
replies
2.0k
views
Is Biopython a Package or Library?
Biopython Python
updated 2.8 years ago by 45k • written 4.4 years ago by ▴ 140
2
votes
2
replies
1.1k
views
Genes with identical reads mapping values across all samples - Kallisto
gene Kallisto expression
updated 4.4 years ago by 56k • written 4.4 years ago by 3.9k
0
votes
0
replies
857
views
Compare segment data produced by CopywriteR and similar tools
copywriter cna
4.4 years ago by Ram 45k
1
vote
1
reply
697
views
R libraries to match SNPs by positions (including switching and flipping)
R Bioconductor SNP
updated 4.4 years ago by 45k • written 4.4 years ago by ▴ 20
3
votes
2
replies
1.1k
views
Is anticancer action of HDAC inhibitors - cancer cells specific or it may cause death to other cell types ?
cancer
updated 4.4 years ago by 27k • written 4.4 years ago by ▴ 220
0
votes
0
replies
658
views
How to incorporate the GRM into a mixed linear model
gwas GRM animal_model
4.4 years ago by DIMITRIOS • 0
0
votes
0
replies
1.9k
views
Job: Group Leader Computational Cancer Biology - VIB-KU Leuven, Belgium
vib groupleader cancer biology computational
4.4 years ago by leen.notebaert • 0
0
votes
4
replies
1.6k
views
sequence similarity
blast linux fasta
updated 4.4 years ago by 22k • written 4.4 years ago by • 0
0
votes
3
replies
3.5k
views
Tassel5v2 vcf file with 'N' in reference and alternate allele
Tassel5v2 SNPcalling GBS
updated 4.4 years ago by • 0 • written 5.9 years ago by ★ 1.1k
0
votes
0
replies
690
views
Calculate accuracy for a Cox model in R
accuracy cox prediction survival R
4.4 years ago by nolwenn ▴ 10
121,890 results • Page 668 of 2438
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How to Identify Conserved 21-mers Across TE Insertions in Drosophila?
How to Identify Conserved 21-mers Across TE Insertions in Drosophila?
Answer: Rna-seq data
Answer: What Are Your Most-Used Public Data Repositories?
Answer: activity of unloaded/unassembled Tn5
Comment: Converting Ensembl Gene Ids To Hgnc Gene Name / Coordinates
Comment: RTG (Real Time Genomics) docker image - Problem dealing with different VCFs
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Comment: Variant analysis for mouse WES by GenoMax 153k
You could open a new issue and ask the developers of `maftools` if this was something they can add.
Comment: How to Identify Conserved 21-mers Across TE Insertions in Drosophila? by GenoMax 153k
Do you have the locations/sequence of the regions you are interested in?
Comment: magpurify errors by shevch2009 ▴ 20
Thank you
Comment: magpurify errors by Mensur Dlakic ★ 30k
To me that sounds like an error in sequence header formatting. Maybe some contig headers are repeated? Or their sequences are short or miss…
Comment: magpurify errors by shevch2009 ▴ 20
Thanks What about phylo-markers module error, I tried to look for it :) But haven't found anything. And why it's not working for some but …
Answer: magpurify errors by Mensur Dlakic ★ 30k
A general answer is to always Google the error message. Hopefully you do that in the future. This is the outcome of Googling `AttributeErro…
Comment: Splice junctions plots for long-read seq data by LChart 5.1k
IGV can view coverage and splice junction sashimi plots. However the plot in the paper looks like it was made with miso. https://miso.readt…
Comment: Yeast reference-based genome assembly by GenoMax 153k
> The gene originates from yeast, What does this mean? Are you putting a gene from a different genus/species into some other yeast? Can yo…
Comment: Variant analysis for mouse WES by alba • 0
Hi, thanks for the suggestion! I’m aware of Ensembl VEP, and in fact, I already have my VCFs annotated with VEP. The challenge I’m facing i…
Answer: Structural Variant identification on pangenome graphs by colindaven 7.9k
There might be something here for you : https://github.com/colindaven/awesome-pangenomes Otherwise, I know creating a pangenome with `mi…
Comment: replace gene names in gff file by ja569116 • 0
Hi @juke34 Is it possible to specify the prefix/ custom gene name to rename all the genes in the gff3 file with AGAT, so that the differen…
Answer: Yeast reference-based genome assembly by colindaven 7.9k
Nanopore reads are long enough to create a full assembly. Why not first try to create a whole genome assembly with a tool like Flye if you …
Comment: Variant analysis for mouse WES by alba • 0
I saw that but it looks like it only works for trinucleotideMatrix() specifically, I was looking to be able to generate rainfallPlot(), for…
Comment: RTG (Real Time Genomics) docker image - Problem dealing with different VCFs by stuckinanendlessfebruary ▴ 10
Dr. Jeremy, Thank you sincerely for your time! I wanted to close the loop: the issue appears to have been the RTG Tools Docker image versi…
Answer: Conversion of Gene Name to Ensembl ID by Thanujay S • 0
Hey! A bit late to the party! I’ve built a simple wrapper (named SESC) around biomaRt to streamline Ensembl ID conversions. It supports bot…
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