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122,200 results • Page 622 of 2444
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DAVID database for gene ontology
DAVID geneontology
4.4 years ago by Vaani • 0
11
votes
5
replies
2.1k
views
Publishing RNA sequencing data analysis scripts on Github before or after Publication?
github
4.4 years ago by m.sadman.sakib ▴ 120
1
vote
0
replies
1.1k
views
Job: PhD Candidate, Using Ontologies to build a Knowledge Graph for Molecular Interactions of Nanoparticles (Maastricht/NL)
owl phd knowledge ontology netherlands graph
4.4 years ago by Egon Willighagen 5.4k
0
votes
0
replies
1.4k
views
Job: Postdoctoral Researcher in Bioinformatics/Cheminformatics, using OpenAPI, FAIR, and Docker for predictive toxicology and risk assessment (Maastricht/…
openapi toxicology netherlands postdoc docker
4.4 years ago by Egon Willighagen 5.4k
3
votes
18
replies
5.2k
views
Help creating Deseq2 count matrix from separate files
or Sample matrix
updated 4.4 years ago by 45k • written 4.4 years ago by ▴ 50
0
votes
0
replies
490
views
the mutual information matrix computed from minet R package>1
minet
4.4 years ago by wei • 0
0
votes
0
replies
1.1k
views
GSEA time series analysis - cls file format?
GSEA cls
4.4 years ago by garfield320 ▴ 20
5
votes
2
replies
3.2k
views
BCL2Fastq when I5 index is UMI
UMI bcl2fastq demultiplex
4.4 years ago by ccagg ▴ 60
1
vote
2
replies
6.6k
views
Spike-in normalization with Cut&Tag data
deeptools normalization ChIP-Seq cutandtag
updated 4.4 years ago by 90k • written 5.3 years ago by • 0
1
vote
2
replies
2.1k
views
Haplotype phasing with Beagle on microarray output VCF, tunning suggestions?
beagle phasing microarray
4.4 years ago by jpablo • 0
2
votes
0
replies
803
views
Stringtie on non model organism - how to best proceed for DE analysis?
Salmon Stringtie DESeq transcriptome rna-seq
4.4 years ago by Shred ★ 1.6k
0
votes
0
replies
532
views
Use All Clusters Expression in One Set with User Defined Phenotypes in rank_gene_groups
Scanpy Python
updated 4.4 years ago by 45k • written 4.4 years ago by • 0
0
votes
2
replies
1.3k
views
Annotating draft genome of a Trichomonad species
Trichomonads Genome annotation MAKER FINDER...
updated 4.4 years ago by 56k • written 5.8 years ago by • 0
1
vote
0
replies
683
views
Comparing distribution of microarray data to that of RNA-seq data
distribution
4.4 years ago by english.server ▴ 300
1
vote
4
replies
1.6k
views
3d structure without PDB
python biopython
updated 2.7 years ago by 45k • written 4.4 years ago by • 0
3
votes
3
replies
1.2k
views
P value signficancy
GEO GEO2R
updated 2.8 years ago by 45k • written 4.4 years ago by ▴ 20
1
vote
1
reply
2.1k
views
Comparison of ratio of expression between two genes across samples
RNA-Seq TPM normalization relative abundance
updated 4.0 years ago by ▴ 80 • written 5.1 years ago by ▴ 20
1
vote
4
replies
1.7k
views
Isoseq3 : Floating point exception
PacBio isoseq
updated 4.4 years ago by 154k • written 4.4 years ago by ▴ 20
0
votes
0
replies
897
views
How to add optional parameters to the Rest API VEP query
API ensemble VEP REST
4.4 years ago by davidjohngreen • 0
3
votes
7
replies
2.1k
views
Get per-nucleotide mapping position for each mapped reads from bam file
mapping nucleotide position
4.4 years ago by Changhao Li • 0
2
votes
2
replies
1.5k
views
An issue in creating a bubble plot using ggplot2
blubbleplot ggplot2 issue
updated 3.1 years ago by ★ 1.7k • written 4.4 years ago by • 0
0
votes
0
replies
883
views
Co-binning with Metabat2, how do I map my reads with BWA?
Metabat2 Co-binning BWA
4.4 years ago by howla1ke • 0
0
votes
7
replies
2.5k
views
How to extracts variants from multiple sequence alignment files?
clustalw biopython fasta fastq
updated 4.4 years ago by 22k • written 4.4 years ago by ▴ 20
2
votes
6
replies
2.3k
views
Issue with htseq-count in Ubuntu
htseq-count htseq NoneType ubuntu encode
updated 4.4 years ago by 35k • written 4.4 years ago by ▴ 20
6
votes
4
replies
2.6k
views
Which covariates include in the differential expression analysis
covariates expression differential deseq2 analysis R
updated 4.4 years ago by ★ 1.3k • written 4.4 years ago by ▴ 30
2
votes
6
replies
1.8k
views
Is there a different names.dmp file in the taxonomy name/id browser?
ncbi
updated 4.4 years ago by 154k • written 4.4 years ago by ▴ 260
1
vote
5
replies
5.9k
views
SingleR annotation of seurat clusters
seurat singleR 10x
updated 4.4 years ago by ★ 19k • written 4.4 years ago by ▴ 40
0
votes
0
replies
688
views
How to choose the heaviest path by calculating the “compatible fragments” in StringTie?
path fragment StringTie compatible heaviest algorithm
4.4 years ago by karta2194512 • 0
0
votes
1
reply
698
views
gene calssfication based on on their chemical nature
RNA-Seq SingleCellSignalR
updated 4.4 years ago by ★ 1.7k • written 4.4 years ago by ▴ 130
1
vote
1
reply
937
views
RS numbers and "novelty"
biomaRt WGS ensembl SNP
updated 4.4 years ago by 24k • written 4.4 years ago by • 0
1
vote
2
replies
1.2k
views
Plot Blastn.table file on R
blastn gRNA Plotting R
4.1 years ago by Sbrillo ▴ 10
0
votes
0
replies
866
views
Job: Postdoc bioinformatics - epigenomics of food allergy risk - Berlin, Germany - 3 years - Ref: DM.124.21b
epigenome postdoc allergies machine-learning
updated 2.7 years ago by 45k • written 4.4 years ago by • 0
2
votes
3
replies
1.2k
views
Blastn for gRNA characterization in ANopheles
Anopheles NCBI gRNA blastn
updated 4.4 years ago by 154k • written 4.4 years ago by ▴ 10
1
vote
3
replies
3.8k
views
Get REVEL plugin started with VEP
VCF REVEL VEP
updated 4.3 years ago by • 0 • written 4.4 years ago by ▴ 110
4
votes
5
replies
1.9k
views
How to paralle trim_galore for single sample?
trim_galore
updated 4.4 years ago by 90k • written 4.4 years ago by ▴ 140
0
votes
0
replies
943
views
How to calculate and visualized alpha and beta diversity from metagenome assembled genome data
diversity phyloseq ggplot R
4.4 years ago by Roland • 0
0
votes
1
reply
1.0k
views
GSEA error 1005
GSEA
updated 17 months ago by 45k • written 4.4 years ago by • 0
2
votes
3
replies
6.1k
views
R ---issues. on server. BiocManager", "genefilter"
BiocManager genefilter
updated 4.4 years ago by ★ 4.8k • written 4.4 years ago by ▴ 50
2
votes
2
replies
2.0k
views
Is there a way to bulk download orthologue pairwise alignment data from ensembl?
alignment orthologue pairwise ensembl
4.4 years ago by theo • 0
0
votes
0
replies
923
views
How to understrand the library complexity
ATAC-seq DNase-seq NGS
4.4 years ago by octpus616 ▴ 120
0
votes
0
replies
1.1k
views
Job: Novo Nordisk Foundation PhD scholarship in the Evolution of Genetic Heterogeneity during Fermentation Process Scale-up
chemical microbiology Fermentation engineering
4.4 years ago by info ▴ 90
3
votes
6
replies
2.3k
views
Ensembl encoding problem
Ensembl encoding
updated 2.7 years ago by 45k • written 4.4 years ago by ▴ 20
1
vote
2
replies
1.9k
views
Many TLENs in a SAM file seem much too big
NGS SAM comperative-genomics alignment
updated 4.4 years ago by ★ 3.0k • written 4.4 years ago by ▴ 70
0
votes
4
replies
2.8k
views
Issue with samtools reheader, bam file
samtools chromosome BAM reheader notation
updated 4.4 years ago by ★ 3.0k • written 4.4 years ago by ▴ 10
0
votes
0
replies
1.2k
views
Error in cvr.glmnet(): formal argument "x" matched by multiple actual arguments
LASSO glmnet R ipflasso
4.4 years ago by lluc.cabus ▴ 30
2
votes
4
replies
5.9k
views
BAM File, Change chromosome notation
samtools chromosome header BAM notation
updated 4.4 years ago by ★ 3.0k • written 4.4 years ago by ▴ 10
0
votes
2
replies
1.1k
views
Intra-dataset (Single Dataset) Batch Correction Tips for scRNA-seq
scrna-seq batch-effect-correction
4.4 years ago by ksaunders73 ▴ 10
0
votes
3
replies
1.3k
views
strand-specific RNA-seq analysis
RNA-seq lncRNA mRNA
updated 4.4 years ago by ★ 1.3k • written 4.4 years ago by ▴ 30
0
votes
0
replies
723
views
chip seq data .narrow dataset
TF narrow from intensity chip
updated 4.4 years ago by 154k • written 4.4 years ago by ▴ 70
7
votes
6
replies
3.1k
views
What is the best practice for analysing single-cell data with low sequencing depth?
10X depth scRNA-seq Sequencing Seurat data
4.4 years ago by VolEr ▴ 40
122,200 results • Page 622 of 2444
Recent Votes
Can EdgeR of DeSeq be used for Single-cell RNA-seq?
Answer: Getting the overlap between two GTF files
Comment: strong appearing variant not found by haplotypecaller in -ERC mode and deepvaria
Converting GFF to GTF
Answer: best practice for diploid variant calling
Answer: Can i use orthofinder for small protein datasets and not full proteome?
Comment: Can i use orthofinder for small protein datasets and not full proteome?
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Recent Replies
Comment: strong appearing variant not found by haplotypecaller in -ERC mode and deepvaria by thomas.heigl.ibk ▴ 10
thanks for the quick reply. i posted the screenshot. gatk-internally, there is still the difference using -ERC or not, priot is getting …
Comment: strong appearing variant not found by haplotypecaller in -ERC mode and deepvaria by thomas.heigl.ibk ▴ 10
here the igv view. showing the histogram for all samples plus the reads for one: ![enter image description here][1] and expanded view of …
Comment: low quality data or file name swapping -- cellranger arc errors when processing by Arup Ghosh 3.5k
Check the read lengths to make sure the files are correct.
Comment: strong appearing variant not found by haplotypecaller in -ERC mode and deepvaria by Pierre Lindenbaum 166k
> Any suggestions or help you could share please, show us an IGV screenshot of the position GATK realign the reads locally, discards read…
Comment: Can i use orthofinder for small protein datasets and not full proteome? by alexandrakortsi • 0
By sequence. Thank you for your response!
Comment: Why did the QV value decrease significantly after using YAHS for HiC scaffolding by xinguok794 ▴ 10
Thank you for your reply! Unfortunately, despite running YAHS with `--no-contig-ec`, the QV value of the resulting FASTA file did not impro…
Comment: Subsetting before QC in Spatial Transcriptomics by Kent ▴ 30
Hi Kevin, Thanks for the detailed explanation. Due to the characteristics of the datasets, we initially used very lenient quality control…
Comment: Midpoint rooting IQTREE newick file moves node support around by Luca Arbore ▴ 10
Thank you very much Kevin, it worked!
Comment: ID unifiying across different datasets by GenoMax 154k
In this case the entry notes that this is likely the product of a pseudogene: https://www.uniprot.org/uniprotkb/Q5VTE0/entry and existence …
Comment: Comparison of different RNAseq data sets by DrSmad ▴ 10
Each lab contributes both control and LPS. Example, for cell line A_lab1 did and analysis on control and LPS-6h. Cell line B_lab2 did contr…
Comment: ID unifiying across different datasets by zizigolu ★ 4.4k
sorry, why some gene names are often lacking though the Uniprot ID is still valid (using biomart)?
Comment: snpEff: Unsupported structural variant types by shpak.max ▴ 70
Unfortunately, while it ran without a problem initially, when I checked the run screen today, I saw the following error message (and unlike…
Comment: ID unifiying across different datasets by GenoMax 154k
You can use the [**ID mapping tool**][1] from UniProt site (third ID did not map from the list above): From To P68104 ENSG0000015…
Answer: The geo samples is not having sentrix id and sentrix position. But this informat by yura.grabovska ▴ 890
Crosspost from related question: https://www.biostars.org/p/9616466/#9616534 ``` ##Using R, illuminaio from Bioconductor library(…
Answer: Finding Sentrix ID in HM450K arrays by yura.grabovska ▴ 890
``` ##Using R, illuminaio from Bioconductor library(illuminaio) temp.idat <- readIDAT(file = "200379120087_R02C02_Grn.idat") tem…
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