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1,000 results • Page 2 of 20
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3
votes
2
replies
6.0k
views
Hypergeometric test of gene set enrichment - Calculate P-value for multiple gene sets in one script?
next-gen R GO
updated 11 months ago by 38k • written 8.2 years ago by ▴ 20
2
votes
1
reply
6.0k
views
BEDgraph to BED/bam
bed
updated 5 months ago by 38k • written 7.6 years ago by ▴ 60
1
vote
7
replies
6.0k
views
Panther pathway Database
gene
updated 8 months ago by 38k • written 7.2 years ago by • 0
6
votes
13
replies
5.9k
views
DESeq2 and edgeR - no agreement between results
RNA-Seq edgeR DESeq2
updated 7 months ago by 38k • written 7.3 years ago by ▴ 60
2
votes
10
replies
5.9k
views
fq.gz file use
BioEdit R
updated 10 days ago by 38k • written 4.1 years ago by • 0
3
votes
1
reply
5.9k
views
how is the output of bcftools stats calculated?
bcftools
updated 6 months ago by 38k • written 7.6 years ago by ▴ 20
4
votes
3
replies
5.9k
views
PLINK2 association study using covariate regression model
SNP plink software-error genome
updated 9 months ago by 38k • written 8.0 years ago by ▴ 20
2
votes
5
replies
5.9k
views
How to normalize gene expression values for finding similar genes
gene RNA-Seq
updated 8 months ago by 38k • written 7.9 years ago by ▴ 10
0
votes
1
reply
5.8k
views
SNP and gene density along the chromosomes plots
gene-density ggplot2 R SNP
updated 10 months ago by 38k • written 7.4 years ago by ▴ 430
1
vote
6
replies
5.8k
views
bedGRAPH files from MACS2 ChIP-seq analysis don't reflect peaks called in peak.xls file
ChIP-Seq
updated 6 months ago by 38k • written 7.5 years ago by ▴ 470
6
votes
7
replies
5.8k
views
best alignment tool for Ion Torrent data
chloroplast genome iontorrent
updated 7 months ago by 38k • written 7.3 years ago by ★ 2.3k
2
votes
1
reply
5.8k
views
Reads, Cluster Numbers, Study Design Comparison
cluster-number Read
updated 8 months ago by 38k • written 7.1 years ago by ▴ 10
0
votes
1
reply
5.8k
views
PLINK: Unrecognized flag '--list-duplicate-vars'
IBD BEAGLE PLINK
updated 11 months ago by 38k • written 8.2 years ago by ▴ 580
1
vote
1
reply
5.8k
views
different color for highlighting genes in Manhattan plot in qqman
R genome
updated 6 months ago by 38k • written 7.5 years ago by ▴ 40
3
votes
4
replies
5.7k
views
HTSeq-count, problem in handling PE data
RNA-Seq HTSeq
updated 7 months ago by 38k • written 7.3 years ago by • 0
3
votes
6
replies
5.7k
views
concordant pair alignment rate is too low
RNA-Seq sequencing alignment
updated 8 months ago by 38k • written 7.1 years ago by ★ 4.1k
1
vote
1
reply
5.7k
views
Error: expecting string instruction after `rep' after typing in "make"
kmergenie
updated 6 months ago by 38k • written 7.4 years ago by • 0
1
vote
9
replies
5.7k
views
downloading nt databases - cannot extract them all?
NCBI blast nt BLAST-plus database
updated 10 months ago by 38k • written 8.0 years ago by ▴ 10
5
votes
3
replies
5.6k
views
GATK "We encountered a non-standard non-IUPAC base in the provided reference: '13"
GATK
updated 7 months ago by 38k • written 7.4 years ago by ▴ 20
4
votes
11
replies
5.6k
views
Correct way to calculate VAF (Variant allele fraction) from a VCF file
VCF snp
7 months ago by prasundutta87 ▴ 650
1
vote
5
replies
5.6k
views
What is mutation calling in exome sequencing?
Exome Mutation-calling SNP-calling Variant-calling
updated 7 months ago by 38k • written 7.3 years ago by ▴ 350
0
votes
3
replies
5.6k
views
Setting dimensions of barplot area in R (for STRUCTURE-like plot)
R
updated 5 months ago by 38k • written 7.6 years ago by ▴ 720
1
vote
1
reply
5.6k
views
vcf SNP file minor allele frequency filter?
vcf minor-allele SNP vcftools
updated 5 months ago by 38k • written 7.6 years ago by ▴ 130
3
votes
6
replies
5.6k
views
Undefined References From Boost When Installing Bam-Readcount
bam-readcount
updated 8 months ago by 38k • written 9.2 years ago by ▴ 10
1
vote
3
replies
5.6k
views
spades; Failed to align paired reads
Assembly
updated 8 months ago by 38k • written 7.2 years ago by ▴ 10
5
votes
4
replies
5.5k
views
HGNC gene symbols
gene ensembl hgnc
updated 7 months ago by 38k • written 7.2 years ago by ▴ 20
1
vote
5
replies
5.5k
views
Converting text format Mass spectrometry data to mzXML?
mass spectrometry data formats mzXNL ASCII
updated 3 months ago by 38k • written 7.7 years ago by • 0
8
votes
2
replies
5.5k
views
Differential gene expression analysis in Python
python R
updated 6 weeks ago by 38k • written 17 months ago by ▴ 30
1
vote
8
replies
5.5k
views
How to update rlang in R?
rlang R
5 months ago by Amr ▴ 140
2
votes
0
replies
5.4k
views
Kraken output to Krona Tools: What can be selected as magnitude
Kraken magnitude Krona
updated 11 months ago by 38k • written 8.1 years ago by ▴ 360
9
votes
1
reply
5.4k
views
Why does MACS2 report multiple records for the same peak region?
ChIP-Seq macs macs2
updated 7 months ago by 38k • written 7.4 years ago by ★ 3.4k
3
votes
4
replies
5.4k
views
How to convert Affymetrix SNP IDs to dbSNP rs SNP names
PLINK SNP genome Affymetrix
updated 7 months ago by 38k • written 7.5 years ago by ▴ 20
1
vote
7
replies
5.4k
views
Converter for GFF file downloaded from NCBI to GTF
annotation gff gtf eval
updated 8 months ago by 38k • written 7.1 years ago by ▴ 20
1
vote
1
reply
5.4k
views
GtfToGenePred errors in converting GTF files.
software-error
updated 3 months ago by 38k • written 7.7 years ago by ▴ 100
1
vote
7
replies
5.4k
views
extract sequences ID from a fasta file
extract sequencesID
updated 10 months ago by 38k • written 8.1 years ago by ▴ 230
3
votes
3
replies
5.3k
views
R - Merge 2 network with different color nodes
merge R networks
updated 6 months ago by 38k • written 7.5 years ago by ▴ 270
1
vote
4
replies
5.3k
views
Why wont my newick file from MEGA open in FigTree?
software error phylogenetic tree MEGA FigTree
updated 5 weeks ago by 20k • written 3.4 years ago by ▴ 10
1
vote
4
replies
5.3k
views
Error when trying to install a package (non-zero exit status)
Packages Bioconductor
updated 10 months ago by ★ 1.0k • written 10 months ago by • 0
1
vote
0
replies
5.3k
views
ANNOVAR vs VEP
SNP
updated 10 months ago by 38k • written 8.0 years ago by ▴ 600
1
vote
9
replies
5.3k
views
SCTransform prior or after merging samples into one object?
Seurat scRNAseq merging samples
updated 12 months ago by ▴ 690 • written 2.5 years ago by • 0
1
vote
6
replies
5.2k
views
output SAM file from STAR aligner looks incomplete
DNAseq alignment aligner STAR
updated 7 months ago by 38k • written 7.3 years ago by ▴ 90
1
vote
3
replies
5.2k
views
How to convert a .gbff to the .gbk using batch method (to do it computationally for several bacteria)
gbff genome gbk
updated 10 days ago by 38k • written 5.4 years ago by ★ 3.9k
9
votes
4
replies
5.2k
views
How to analyse normalized read count?
RNA-Seq R
updated 11 weeks ago by 38k • written 7.8 years ago by ▴ 150
1
vote
0
replies
5.2k
views
additive and multiplicative genetic models in logistic regression
SNP
updated 7 months ago by 38k • written 7.4 years ago by ▴ 10
5
votes
1
reply
5.2k
views
Generating Gencode TSS file
gencode tss
updated 7 months ago by 38k • written 7.3 years ago by ▴ 210
2
votes
1
reply
5.2k
views
WGCNA - problems picking a suitable power
RNA-Seq pickSoftThreshold WGCNA power
updated 8 months ago by 38k • written 7.1 years ago by ▴ 50
10
votes
15
replies
5.2k
views
convert fasta/gb to vcf
fasta vcf genbank gff
updated 5 days ago by 38k • written 4.5 years ago by ▴ 670
3
votes
1
reply
5.1k
views
Calculating Watterson's Theta and Tajima's Pi from NGS (bam file)
NGS theta pi bam SNP
updated 11 months ago by 38k • written 8.1 years ago by ★ 2.6k
1
vote
2
replies
5.1k
views
Snpsift extractFields : How Fields Annotation ANN[*].XX is working ?
vcf Snpeff annotation
updated 7 months ago by 38k • written 7.2 years ago by ▴ 500
4
votes
3
replies
5.1k
views
Comparing 2 gene lists
gene
updated 9 months ago by 38k • written 8.0 years ago by ▴ 40
1,000 results • Page 2 of 20
Recent Votes
A: In Seurat, How Do nCount_RNA Differ from nFeature_RNA?
smoothing or binning bigWig file
List of Ongoing and Planned Long Read Sequencing studies?
Are We Rude/Do We Expect Too Much From People Asking Questions On This Forum?
Answer: Read lengths greater than insert length
A: Changing Output From Gene ID to Symbol When Running findMarkers from Scran
Answer: BLAST Database error: No alias or index file found for nucleotide database
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Recent Replies
Comment: split fasta file to train deep learning model by shenwei356 7.9k
Excluding sequences containing any letter not belonging to the 20 [amino acids letters](https://github.com/shenwei356/bio/blob/master/seq/a…
Comment: split fasta file to train deep learning model by pinheirofabiano ▴ 10
@shenwei356, thank you very much for your help, perfect! But now I realized that some fasta sequences contain the letter "B", which is ou…
Comment: Most efficient way to run Diamond against a very very large database (i.e., NCBI by Mensur Dlakic ★ 23k
I think it depends on the speed of your local disks and the memory amount. On a single node, breaking up the database doesn't sound like a …
Comment: Sample size for population genetics by Jeremy Leipzig 21k
Other populations just make the model harder to generalize, not easier.
Comment: Are We Rude/Do We Expect Too Much From People Asking Questions On This Forum? by Vincent Laufer ★ 2.5k
i think there is some of that - my most upvoted comment of all time was a dismissive comment i made while extremely tired. for context i ha…
Comment: Molecular biologist / clinical pharmacologist (f/m/d) by Jeremy ▴ 770
Is this job on site in Vienna or remote?
Comment: smoothing or binning bigWig file by rls_08 ▴ 40
if you use bigwigCompare , that would not create a sliding window, but instead, it will output the mean for each bin, according to the -bin…
Comment: Sample size for population genetics by zimmer.schweiz • 0
Thank you so much for your answer. For common polygenic diseases, would it make sense to increase the number of populations sampled, in ord…
Answer: Sample size for population genetics by Jeremy Leipzig 21k
For a rare penetrant monogenic disease? A few cases. For a common polygenic disease or trait? 500k-10M
Answer: using GRanges metadata to constrain overlap searches between objects by seidel 11k
Rather than do all overlaps all the time for all samples, why not restrict the data by sample when you can. The code below works about 4 ti…
Comment: How to get gene from PSIBLAST resuts by Tom • 0
Hello, thank you for your answer, I have a question, Why the information from the GFF file and from the feature table is different? I see …
Comment: SNP ID (rsID) to Chr no. and Position by Jewahir • 0
Yeah, thank you for that!!
Comment: 1000 genomes hg38 with dbSNP rsid by Ram 38k
It should be pretty straightforward. Just to save you some pain, run these on the 1000g VCF once you download it: 1. `vt decompose -s` to …
Comment: 1000 genomes hg38 with dbSNP rsid by Vince ▴ 150
Yeah, I had some hope that I wouldn't need to mess with doing this ...
Answer: counting the unmapped reads by chemkhi.ali13 • 0
> Hi all, > > I have a sam file, my supervisor asked me to count the number of > unmapped reads, which command I should use? > > sam…
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