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3
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4
replies
1.4k
views
Divide the dataframe based on conditions in R
R dividing data-frame function
3.2 years ago by KABILAN ▴ 130
0
votes
0
replies
831
views
Job: Postdoctoral Fellow (Quantitative Modeling Group)
Biological Systems
3.2 years ago by BerkeleyLab ▴ 70
6
votes
4
replies
1.4k
views
Figuring out if a gene exists in a genome
gene genome blast
3.2 years ago by chronotope ▴ 10
9
votes
11
replies
2.8k
views
Help needed to troubleshoot a Bioconda recipe for a Rust tool
recipe bioconda rust
3.2 years ago by Matthias Zepper 5.1k
2
votes
7
replies
1.9k
views
headers missing in efetch results for SRA database
SRA Entrez.Direct efetch
updated 3.2 years ago by ▴ 520 • written 3.2 years ago by ▴ 130
1
vote
2
replies
1.0k
views
About hg19 reference genome
hg19 referencegenome
3.2 years ago by luckysardar171 ▴ 20
0
votes
1
reply
572
views
Genotyping tool
genotyping
updated 3.2 years ago by 166k • written 3.2 years ago by • 0
11
votes
3
replies
1.1k
views
parsing the output in to a table format ?
gene aw genome protein
updated 3.2 years ago by 5.1k • written 3.2 years ago by ▴ 1000
0
votes
1
reply
763
views
problem with sequence alignment
peptides alignment
updated 3.2 years ago by ★ 2.1k • written 3.2 years ago by • 0
0
votes
5
replies
3.1k
views
Missing gene symbols in bustools output
bustools scanpy kallisto single-cell scRNA
updated 3.2 years ago by • 0 • written 5.6 years ago by ★ 1.3k
1
vote
2
replies
1.2k
views
vg construct unsupported variant allele
vg graph vcf variantion vgteam
3.1 years ago by Yihang • 0
2
votes
2
replies
950
views
Does the Minion demultiplex when basecalling?
minion minknow long-read
updated 17 months ago by 45k • written 3.2 years ago by • 0
5
votes
6
replies
2.6k
views
How can I biuld to pipeline in nextflow to download SRA files?
nextflow
3.2 years ago by pavelasquezv ▴ 50
2
votes
5
replies
1.4k
views
detection of DNA transpsosons
DNA transposons
3.2 years ago by manaswiniparija3 ▴ 60
0
votes
0
replies
457
views
missingness for chromosome X
bcftools missingness
updated 2.2 years ago by 45k • written 3.2 years ago by • 0
0
votes
0
replies
535
views
how to solve PermissionError: [Errno 1] Operation not permitted during running a MitoZ tool
mitoZ assembly
updated 2.3 years ago by 45k • written 3.2 years ago by ▴ 60
5
votes
2
replies
1.5k
views
Fastq: how can I check if they are from DNA or RNAseq data?
WES Fastq
updated 3.2 years ago by ★ 5.2k • written 3.2 years ago by ▴ 690
0
votes
5
replies
1.4k
views
how to extract DNA seq from a file which contain both protein and DNA
fasta
updated 3.2 years ago by 153k • written 3.2 years ago by ▴ 20
0
votes
2
replies
938
views
How to extract ORF_ID(LR590472.1_162 ) from large number of txt file
fasta
3.2 years ago by Neel ▴ 20
0
votes
0
replies
611
views
Understand the Fields from Illumina Infinium Genotype Report
infinium illumina genotypereport microarray
3.2 years ago by pfee418 ▴ 10
1
vote
0
replies
690
views
Enrichment testing via hypergeometric test
gene gsea Enrichment set
3.2 years ago by KitScorpion ▴ 10
0
votes
3
replies
1.6k
views
Hardy-Weinberg equilibrium analysis in Plink for association study.
Plink association study
updated 3.2 years ago by • 0 • written 3.2 years ago by ▴ 50
0
votes
2
replies
1.1k
views
Joining 'n' number of lists and perform a function in R
lists data_frame R_function R comine_lists
3.2 years ago by KABILAN ▴ 130
1
vote
12
replies
6.9k
views
Picard: EstimateLibraryComplexity -> OutOfMemoryError
java bam picard
updated 3.2 years ago by • 0 • written 11.3 years ago by 11k
1
vote
1
reply
704
views
Detecting heterogeneous X chromosome counts in XXY individual
VCF WGS XXY
updated 3.2 years ago by ▴ 20 • written 3.2 years ago by • 0
0
votes
0
replies
957
views
Circular-Manhattan plot for GWAS
Circular R Rstudio Manhattan plot
3.2 years ago by HaroonPakistan • 0
0
votes
0
replies
556
views
How to remove XTR region from my vcf file.
WGS GWAS VCF
updated 2.8 years ago by 45k • written 3.2 years ago by • 0
0
votes
0
replies
406
views
single-cell Alzheimer's data from studies involving anti-herpetic drugs
alzheimers single-cell
3.2 years ago by Aaron ▴ 30
2
votes
4
replies
1.8k
views
Agilent platform in microarray data analysis
Agilent microarray
3.2 years ago by nishimalhotra2612 ▴ 50
0
votes
0
replies
1.4k
views
Job: Postdoctoral position at Agriculture and Agri-Food Canada (AAFC) - PRP Research Scientist
NGS Research_Scientist genomics AAFC
updated 2.7 years ago by 45k • written 3.2 years ago by • 0
5
votes
12
replies
2.6k
views
How to perform quality control on multiple folders using trimmomatic?
trimmomatic
3.2 years ago by pavelasquezv ▴ 50
0
votes
0
replies
644
views
Invalid number of arguments rsem-calculate-expression
rsem bowtie
3.2 years ago by Patricia • 0
2
votes
4
replies
1.9k
views
Sex determination using bcftools
bcftools sex
updated 2.2 years ago by 45k • written 3.2 years ago by • 0
2
votes
2
replies
929
views
How to learn statistics for multiomics
statistics multiomics
updated 2.7 years ago by 45k • written 3.2 years ago by • 0
2
votes
3
replies
947
views
quantify how many reads detect ORF9 and ORF10
reads ORF9 annotated
3.2 years ago by mkhatun • 0
2
votes
3
replies
3.0k
views
how to download all the human protein sequence at once
database sequence protein
3.2 years ago by salvatore.raieli2 ▴ 90
0
votes
0
replies
634
views
How to update gene annotation file for draft genome assembly using RagTag, improve reads mapping RNA-seq data
draft genome assembly RagTag
3.2 years ago by RS • 0
0
votes
1
reply
1.3k
views
Snakemake Qiime2 caching error
Qiime2 Snakemake
updated 3.2 years ago by ▴ 880 • written 3.2 years ago by • 0
2
votes
8
replies
1.9k
views
VCF file
VCF Bed
3.2 years ago by Nameless • 0
0
votes
1
reply
818
views
SPSS : Descriptive analysis cross tabs error
crosstabs SPSS descriptive analysis
updated 3.2 years ago by ★ 29k • written 3.2 years ago by ▴ 50
0
votes
0
replies
586
views
vg giraffe
variation-graph vg
updated 2.3 years ago by 45k • written 3.2 years ago by ▴ 10
0
votes
3
replies
1.2k
views
Recovering sequencing reads due to Low-Diversity Illumina Sequencing Libraries
Illumina mini-seq
updated 3.2 years ago by 153k • written 3.2 years ago by ★ 1.5k
10
votes
2
replies
1.3k
views
Best NGS Bioinformatics Blogs (2022)
research knowledge
updated 2.6 years ago by 45k • written 3.2 years ago by 11k
0
votes
2
replies
1.1k
views
Bowtie2 penality scoring
scoring Bowtie2
3.1 years ago by kiran ▴ 10
0
votes
6
replies
1.9k
views
VEP synonyms file
Ensembl-VEP annotation synonyms
3.2 years ago by Sowmya Pulapet ▴ 70
1
vote
7
replies
1.9k
views
Script or tool to compare more than two .cls files in R or Python
R Python
updated 3.2 years ago by 22k • written 3.2 years ago by ▴ 20
0
votes
0
replies
664
views
VEP custom annotation - synonymous file
Ensembl-VEP annotation synonymsfile
3.2 years ago by Sowmya Pulapet ▴ 70
0
votes
0
replies
577
views
SPSS statistics Analysis
quantitative SPSS variable Marker analysis Genotype Clinical
3.2 years ago by Nai ▴ 50
0
votes
0
replies
592
views
POST sequences to pubMLST API
pubmlst restful api
3.2 years ago by davidmaimoun ▴ 50
0
votes
1
reply
630
views
Kallisto loop error
kallisto
updated 2.3 years ago by 45k • written 3.2 years ago by • 0
121,850 results • Page 399 of 2437
Recent Votes
Answer: Cibersortx server down?
Seurat not creating nCount_RNA and nFeature_RNA
Comment: Reading AD and other genotype information from the VCF file
C: How To Split A Bam File By Chromosome
DESeq2 time-series - full model matrix is less than full rank
Answer: RNAseq requirements: Biological and Technical replicates
C: Differential Peaks Between Replicates
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Answer: Seurat not creating nCount_RNA and nFeature_RNA by bczvx1004 • 0
i had same problem today. i fix it with cleaning the workspace and restart the session by pressing the ctrl+shift+F10.
Comment: Issue with renaming genes in expression matrix for heatmap in R by rfran010 ★ 1.6k
Maybe I'm missing something, it seems your recode function is switching values in a vector and then you later try to subset based on the ne…
Comment: Reading AD and other genotype information from the VCF file by Pierre Lindenbaum 166k
`bcftools query -f '[%CHROM %POS %REF %ALT %SAMPLE %GT %AD\n]' `
Comment: Tools for raw reads that estimate the percentage of reads that hit marker genes by colindaven 7.8k
This one has the massive computing resources at the EBI behind it, so I wouldn't worry about capacity. Check their stats.
Answer: Cibersortx server down? by GenoMax 153k
Yes it is down now (though it was working ~ 3-4 hours ago): https://downforeveryoneorjustme.com/cibersortx.stanford.edu?proto=https
Answer: Available signature matrix for deconvoluting my bulk data using CIBERSORTX by Sam • 0
Have you checked out [cellxgene][1]? If you filter by organism you might find one that is suitable. [1]: https://cellxgene.cziscience.c…
Comment: RNAseq requirements: Biological and Technical replicates by jkim ▴ 220
Ouch, my mistake. Updated my comment.
Comment: RNAseq requirements: Biological and Technical replicates by i.sudbery 22k
However, one might argue that multiple biological samples (i.e. multiple blood draws) from each patient might be useful. Still, probably no…
Comment: Tools for raw reads that estimate the percentage of reads that hit marker genes by Mensur Dlakic ★ 29k
> So maybe this approach will help us find interesting and rare pathways — something along those lines. Still the same answer as before - …
Comment: ATAC-seq fragment size distribution - huge spike at 150 bp by yuntan1992 • 0
or add parameter "--soft-clipped-unmapped-tlen"
Comment: CIBERSORTx error: 'x' must be an array of at least two dimensions by ATpoint 89k
I would take this opportunity to encourage using different tools. Cibersortx is not open, its source code has never been published. That ha…
Answer: CIBERSORTx error: 'x' must be an array of at least two dimensions by catarinaventura_pt • 0
For those still looking for the answer about this, I just figured out that you need to have replicates for it to work.
Comment: CIBERSORTx error: 'x' must be an array of at least two dimensions by catarinaventura_pt • 0
I´m having the same problem here described. Any updates on how to solve this?
Answer: ATAC-seq fragment size distribution - huge spike at 150 bp by yuntan1992 • 0
After removing adapters with trim_galore, change the parameter of bowtie2 " --local" to "--end-to-end".
Comment: Tools for raw reads that estimate the percentage of reads that hit marker genes by shevch2009 ▴ 20
That is a great comparison! :) It definitely looks that way. :) It's not about taxonomy, but about reconstructing metabolic pathways direc…
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