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122,018 results • Page 592 of 2441
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Download UniProt databases via HTTP/HTTPS instead of FTP? (Google Apps Scripts Question)
UniProt Databases Google FTP sequence
updated 4.1 years ago by ▴ 760 • written 8.2 years ago by ▴ 30
1
vote
1
reply
1.1k
views
How to merge multiple patient's vcf files (indel and snv) with different IDs?
vcf gatk
updated 4.1 years ago by ★ 3.0k • written 4.1 years ago by ▴ 110
0
votes
0
replies
627
views
Point pattern analysis - functions
colocalization programming imaging
4.1 years ago by Hashirama ▴ 20
1
vote
3
replies
1.5k
views
MD plot for every sample (?!)
MD-plot EdgeR
4.1 years ago by Barista ▴ 60
1
vote
1
reply
1.2k
views
Difference between linear and log2 CNA values
cna linear log2
updated 4.1 years ago by 45k • written 4.1 years ago by • 0
1
vote
2
replies
2.9k
views
Tutorials for Robust Rank Agrregation
RNA-Seq R next-gen-sequencing
updated 3.3 years ago by 45k • written 4.1 years ago by ▴ 10
5
votes
3
replies
1.9k
views
Is removing strand information when obtaining intergenic regions from GRanges necessary?
GenomicRanges methylation strand intergenic genic
updated 4.1 years ago by 9.0k • written 4.1 years ago by ★ 1.1k
6
votes
10
replies
4.7k
views
DESeq2 with a small number of genes
DESeq2 SARTools RNA-Seq Count-normalisation
updated 4.1 years ago by ▴ 90 • written 9.0 years ago by ▴ 660
12
votes
7
replies
8.3k
views
6 follow
BAM compression: .tar.gz = same size as before?
bam compression tar gz
updated 4.1 years ago by ▴ 240 • written 8.3 years ago by ▴ 220
18
votes
9
replies
18k
views
8 follow
Downsample BAM file to specific amount of reads
bam
updated 19 months ago by 154k • written 4.2 years ago by ▴ 110
1
vote
2
replies
1.5k
views
Difference between NCBI and mega 6 software based nucleotide sequence alignments
ALIGNMENT NUCLEOTIDE MEGA
4.1 years ago by ashenafymamo • 0
1
vote
2
replies
2.5k
views
samtools returns error - cigar and query sequence are of different length even though cigar and query sequence are the same length
sam samtools bam
4.1 years ago by jennifer.lu • 0
3
votes
2
replies
2.9k
views
Download bigWig files of publicly available ChIP-seq samples
cistrome bigwig chip-seq
4.1 years ago by Friederike 9.0k
0
votes
0
replies
566
views
Degree distribution plot in R with gamma value
distribution degree R
4.1 years ago by jananinithu • 0
2
votes
3
replies
3.1k
views
GATK : VariantRecalibrator no positional argument is defined for this tool.
GATK filtration Variant SNP
3.5 years ago by Arslan Tariq ▴ 140
7
votes
15
replies
3.6k
views
very low coverage when mappin genomic DNA
mapping coverage DNA genomic
updated 4.1 years ago by 89k • written 4.1 years ago by ★ 1.3k
0
votes
0
replies
521
views
Selecting a group of cells expressing a list of genes
sc-rna sequencing
4.1 years ago by Lekshmy ▴ 10
0
votes
0
replies
627
views
How to determine exact tRNA sequence
annotation
4.1 years ago by wes ▴ 90
0
votes
1
reply
934
views
gromacs returns out of memory error in NVT equilibration step
simulation gromacs NVT equilibiration
updated 4.1 years ago by ▴ 320 • written 4.1 years ago by ▴ 20
1
vote
2
replies
2.1k
views
how to solve this error when I want to install HISAT2? "E: Unable to locate package hisat2"
hisat2 aligner
4.1 years ago by modarzi ▴ 170
2
votes
6
replies
3.4k
views
SNP Pruning Through PCA (Edit: Feature Selection Through PCA)
PLINK SNP PCA
updated 2.6 years ago by 45k • written 4.1 years ago by • 0
0
votes
2
replies
1.7k
views
VisCello Shiny app code for hosting snRNA-seq data
shiny scRNA-seq snRNA-seq VisCello
updated 4.1 years ago by 45k • written 4.5 years ago by ▴ 30
1
vote
3
replies
2.0k
views
Whether the probe intensity of microarray can be used to calculate TPM like the count data of RNAseq?
microarray RNAseq
updated 3.7 years ago by ★ 8.3k • written 4.1 years ago by ▴ 10
1
vote
1
reply
1.0k
views
How to graphically represent a known DNA motif in a list of DNA sequences
sequences DNA motif representation
updated 4.1 years ago by 36k • written 4.1 years ago by ▴ 30
2
votes
1
reply
1.9k
views
How to load Seurat Object into WGCNA Tutorial Format
seurat wgcna
4.1 years ago by ksaunders73 ▴ 10
4
votes
5
replies
2.4k
views
Calculate fold change in edgeR with one sample per condition
R edgeR expression rna-seq differential
4.1 years ago by mohammedtoufiq91 ▴ 270
8
votes
6
replies
7.1k
views
How to convert log2 scale RNA-Seq expression data to linear scale data
expression edgeR R rna-seq fold-change
updated 4.2 years ago by 13k • written 4.2 years ago by ▴ 270
0
votes
2
replies
2.0k
views
Circos plot with logfold change RNA seq data
circos
updated 2.6 years ago by 45k • written 4.1 years ago by • 0
3
votes
9
replies
3.2k
views
DESeq2 design
coldata DSeseq2 featureCounts design DESeqDataSetFromMatrix
4.1 years ago by Rajesh ▴ 10
1
vote
0
replies
834
views
what's the criteria to select true-positive miRNAs predicted by miRDEEP2?
miRDEEP2 true-positive criteria
4.1 years ago by weixuchu63 ▴ 10
1
vote
3
replies
1.4k
views
About runing Pilon on individual chromosomes when polish draft genome assembly
Pilon chromosome polish genome draft
updated 17 months ago by ▴ 190 • written 4.1 years ago by ▴ 80
1
vote
5
replies
2.9k
views
how to combine either Rna-seq datasets or results from analysis of Rna-seq datasets to get a visual result
RNA-Seq next-gen-sequencing
updated 3.3 years ago by 45k • written 4.1 years ago by ▴ 10
0
votes
4
replies
3.4k
views
BLAST masking
masking database blastp
4.1 years ago by timothy.kirkwood ▴ 140
1
vote
2
replies
1.4k
views
WGS bacterial metagenomic pipeline - group comparison
metagenomics WGS pipeline bacterial
4.1 years ago by predeus ★ 2.1k
1
vote
7
replies
3.2k
views
Difficulty Using FastX Toolkit on Mac
mac unix ngs fastx executable
updated 4.1 years ago by 89k • written 4.1 years ago by • 0
0
votes
0
replies
658
views
Metadata for splice variant VCF
VCF Splice Variant
4.1 years ago by Varun • 0
0
votes
7
replies
3.0k
views
FreeBayes VCF output with FORMAT unknown
VCF FreeBayes unknown FORMAT
4.1 years ago by Michal Nevo ▴ 140
0
votes
2
replies
2.6k
views
When importing my quant.sf files into R using tximport, should I set 'ignoreTxVersion' to True or False?
Salmon RNA-Seq tximport R
updated 4.1 years ago by ▴ 270 • written 4.1 years ago by • 0
0
votes
0
replies
1.1k
views
Annotation Forge Error: makeOrgPackageFromNCBI
annotation forge
4.1 years ago by Trinh ▴ 10
0
votes
2
replies
2.1k
views
Calculate TPM values from DESeq2 normalised counts
RNA-Seq
4.1 years ago by James Cook • 0
0
votes
0
replies
866
views
Plotting curves from multi-state models using survminer
survminer survival multi-state analysis models
4.1 years ago by Kamran • 0
1
vote
2
replies
1.3k
views
Convert gff3 (or .out file) in RepeatMasker into tbl format
RepeatMasker gff3 tbl
4.1 years ago by katak • 0
0
votes
0
replies
747
views
hjust in geom_cladelab not working properly
geom_cladelab R ggtree
4.1 years ago by Søren • 0
1
vote
1
reply
976
views
Conda has been installed - but can't be found file
install terminal miniconda not conda found
updated 4.1 years ago by 89k • written 4.1 years ago by ▴ 20
0
votes
0
replies
1.7k
views
Problems with R (protect() -> stackoverflow)
random RStudio forest
4.1 years ago by Esra • 0
1
vote
4
replies
2.5k
views
Can I sort my bam files with Picard MergeSamFiles?
MergeSamFiles picard-tools SortSam
updated 4.1 years ago by ★ 2.1k • written 4.2 years ago by ▴ 40
0
votes
2
replies
1.4k
views
VEP output is only protein_coding
VEP
4.1 years ago by storm1907 ▴ 30
0
votes
0
replies
819
views
Mapping reads and quantifying genes - Metagenomic workshop
metagenome
4.1 years ago by arshad1292 ▴ 110
3
votes
1
reply
1.1k
views
Extract log2FC values from volcanoplot() possible?
volcanoplot R limma
updated 4.1 years ago by ★ 8.3k • written 4.1 years ago by ▴ 80
0
votes
6
replies
11k
views
How to change the default font in ggplot 2
font ggplot2 Arial
4.1 years ago by camillab. ▴ 160
122,018 results • Page 592 of 2441
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Answer: HIV NL4-3 transcriptome fasta
ORFanage: by-reference protein annotation and comparison for transcriptome assembly
Mugsy Error: Can't find delta file....
A: Mugsy Error: Can't find delta file....
Answer: Variant Normalization
SeqKit: a cross-platform and ultrafast toolkit for FASTA/Q file manipulation in Golang
Answer: 1 vs 1 DEG analysis in scrna seq data
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Answer: Variant Normalization by Istvan Albert 103k
The purpose of normalization is to ensure that identical variants are represented identically. When not normalized, the same variants may …
Answer: Should differential expression analysis be incorporated in cross validation for by i.sudbery 22k
Yes, their would potentially be data leakage if you perform the DE before dividing your datasets into folds. Its unclear how much of a prob…
Comment: Brave: Bioinformatics Reactive Analysis and Visualization Engine by Istvan Albert 103k
I visited the website, but I couldn't understand what problem the software solves. You need to do a much better job of communicating the p…
Comment: Choosing enrichment analysis tool by i.sudbery 22k
How have these gene lists been obtained?
Comment: NOVOPlasty assembly fails with “INVALID SEED” using first read as seed by GenoMax 154k
> I used the first read sequence from ERR322446.filtered.A.fq as the seed `ERR322446` appears to be a human sample. Did you convert the …
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> Each individual Snippy run completes successfully and reports multiple variants When you run `snippy-core` there is no reference provid…
Comment: Quantification using salmon in alignment-based mode after minimap2 run by Assa Yeroslaviz ★ 1.9k
Hi Rob, sorry for the late question. I was wondering though, if I can also quantify transposable elements using oarfish? Should I increas…
Answer: 1 vs 1 DEG analysis in scrna seq data by ATpoint 89k
The only option you have is to treat every single cell as a replicate. That has the obvious downside that any effect can be a donor-unique …
Answer: GUI commercial software for 10x single cell gene expression analysis by firestar ★ 1.7k
An open-source option: [kana](https://www.kanaverse.org/kana/).
Comment: Brave: Bioinformatics Reactive Analysis and Visualization Engine by Edward • 0
Yes, we plan to make English the primary language of the Brave UI.
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?
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