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Job: Postdoctoral Researcher in Bioinformatics/Cheminformatics, using OpenAPI, FAIR, and Docker for predictive toxicology and risk assessment (Maastricht/…
openapi toxicology netherlands postdoc docker
4.2 years ago by Egon Willighagen 5.4k
3
votes
18
replies
4.8k
views
Help creating Deseq2 count matrix from separate files
or Sample matrix
updated 4.1 years ago by 45k • written 4.2 years ago by ▴ 50
0
votes
0
replies
437
views
the mutual information matrix computed from minet R package>1
minet
4.2 years ago by wei • 0
0
votes
0
replies
1.0k
views
GSEA time series analysis - cls file format?
GSEA cls
4.2 years ago by garfield320 ▴ 20
5
votes
2
replies
3.0k
views
BCL2Fastq when I5 index is UMI
UMI bcl2fastq demultiplex
4.2 years ago by ccagg ▴ 60
1
vote
2
replies
6.0k
views
Spike-in normalization with Cut&Tag data
deeptools normalization ChIP-Seq cutandtag
updated 4.2 years ago by 89k • written 5.1 years ago by • 0
1
vote
2
replies
1.9k
views
Haplotype phasing with Beagle on microarray output VCF, tunning suggestions?
beagle phasing microarray
4.2 years ago by jpablo • 0
2
votes
0
replies
741
views
Stringtie on non model organism - how to best proceed for DE analysis?
Salmon Stringtie DESeq transcriptome rna-seq
4.2 years ago by Shred ★ 1.6k
0
votes
0
replies
494
views
Use All Clusters Expression in One Set with User Defined Phenotypes in rank_gene_groups
Scanpy Python
updated 4.2 years ago by 45k • written 4.2 years ago by • 0
0
votes
2
replies
1.2k
views
Annotating draft genome of a Trichomonad species
Trichomonads Genome annotation MAKER FINDER...
updated 4.2 years ago by 56k • written 5.6 years ago by • 0
4
votes
13
replies
40k
views
6 follow
[main_samview] fail to read the header from sample.bam
alignment
updated 3.2 years ago by ▴ 10 • written 7.5 years ago by ▴ 20
1
vote
0
replies
614
views
Comparing distribution of microarray data to that of RNA-seq data
distribution
4.2 years ago by english.server ▴ 300
1
vote
4
replies
1.4k
views
3d structure without PDB
python biopython
updated 2.5 years ago by 45k • written 4.2 years ago by • 0
3
votes
3
replies
1.1k
views
P value signficancy
GEO GEO2R
updated 2.6 years ago by 45k • written 4.2 years ago by ▴ 20
1
vote
1
reply
2.0k
views
Comparison of ratio of expression between two genes across samples
RNA-Seq TPM normalization relative abundance
updated 3.8 years ago by ▴ 80 • written 4.9 years ago by ▴ 20
1
vote
4
replies
1.5k
views
Isoseq3 : Floating point exception
PacBio isoseq
updated 4.2 years ago by 153k • written 4.2 years ago by ▴ 20
0
votes
0
replies
796
views
How to add optional parameters to the Rest API VEP query
API ensemble VEP REST
4.2 years ago by davidjohngreen • 0
3
votes
7
replies
1.9k
views
Get per-nucleotide mapping position for each mapped reads from bam file
mapping nucleotide position
4.2 years ago by Changhao Li • 0
2
votes
2
replies
1.4k
views
An issue in creating a bubble plot using ggplot2
blubbleplot ggplot2 issue
updated 2.9 years ago by ★ 1.7k • written 4.2 years ago by • 0
0
votes
0
replies
831
views
Co-binning with Metabat2, how do I map my reads with BWA?
Metabat2 Co-binning BWA
4.2 years ago by howla1ke • 0
0
votes
7
replies
2.3k
views
How to extracts variants from multiple sequence alignment files?
clustalw biopython fasta fastq
updated 4.2 years ago by 22k • written 4.2 years ago by ▴ 20
2
votes
6
replies
2.0k
views
Issue with htseq-count in Ubuntu
htseq-count htseq NoneType ubuntu encode
updated 4.2 years ago by 35k • written 4.2 years ago by ▴ 20
6
votes
4
replies
2.4k
views
Which covariates include in the differential expression analysis
covariates expression differential deseq2 analysis R
updated 4.2 years ago by ★ 1.3k • written 4.2 years ago by ▴ 30
2
votes
6
replies
1.6k
views
Is there a different names.dmp file in the taxonomy name/id browser?
ncbi
updated 4.2 years ago by 153k • written 4.2 years ago by ▴ 260
1
vote
5
replies
5.6k
views
SingleR annotation of seurat clusters
seurat singleR 10x
updated 4.2 years ago by ★ 19k • written 4.2 years ago by ▴ 40
0
votes
0
replies
617
views
How to choose the heaviest path by calculating the “compatible fragments” in StringTie?
path fragment StringTie compatible heaviest algorithm
4.2 years ago by karta2194512 • 0
0
votes
1
reply
632
views
gene calssfication based on on their chemical nature
RNA-Seq SingleCellSignalR
updated 4.2 years ago by ★ 1.7k • written 4.2 years ago by ▴ 130
1
vote
1
reply
843
views
RS numbers and "novelty"
biomaRt WGS ensembl SNP
updated 4.2 years ago by 24k • written 4.2 years ago by • 0
1
vote
2
replies
1.1k
views
Plot Blastn.table file on R
blastn gRNA Plotting R
3.9 years ago by Sbrillo ▴ 10
0
votes
0
replies
810
views
Job: Postdoc bioinformatics - epigenomics of food allergy risk - Berlin, Germany - 3 years - Ref: DM.124.21b
epigenome postdoc allergies machine-learning
updated 2.5 years ago by 45k • written 4.2 years ago by • 0
2
votes
3
replies
1.1k
views
Blastn for gRNA characterization in ANopheles
Anopheles NCBI gRNA blastn
updated 4.2 years ago by 153k • written 4.2 years ago by ▴ 10
1
vote
3
replies
3.5k
views
Get REVEL plugin started with VEP
VCF REVEL VEP
updated 4.1 years ago by • 0 • written 4.2 years ago by ▴ 110
4
votes
5
replies
1.8k
views
How to paralle trim_galore for single sample?
trim_galore
updated 4.2 years ago by 89k • written 4.2 years ago by ▴ 140
0
votes
0
replies
732
views
How to calculate and visualized alpha and beta diversity from metagenome assembled genome data
diversity phyloseq ggplot R
4.2 years ago by Roland • 0
0
votes
1
reply
984
views
GSEA error 1005
GSEA
updated 14 months ago by 45k • written 4.2 years ago by • 0
2
votes
3
replies
6.0k
views
R ---issues. on server. BiocManager", "genefilter"
BiocManager genefilter
updated 4.2 years ago by ★ 4.8k • written 4.2 years ago by ▴ 50
2
votes
2
replies
1.7k
views
Is there a way to bulk download orthologue pairwise alignment data from ensembl?
alignment orthologue pairwise ensembl
4.2 years ago by theo • 0
0
votes
0
replies
831
views
How to understrand the library complexity
ATAC-seq DNase-seq NGS
4.2 years ago by octpus616 ▴ 120
0
votes
0
replies
977
views
Job: Novo Nordisk Foundation PhD scholarship in the Evolution of Genetic Heterogeneity during Fermentation Process Scale-up
chemical microbiology Fermentation engineering
4.1 years ago by info ▴ 80
3
votes
6
replies
2.1k
views
Ensembl encoding problem
Ensembl encoding
updated 2.5 years ago by 45k • written 4.2 years ago by ▴ 20
1
vote
2
replies
1.7k
views
Many TLENs in a SAM file seem much too big
NGS SAM comperative-genomics alignment
updated 4.2 years ago by ★ 3.0k • written 4.2 years ago by ▴ 70
0
votes
4
replies
2.6k
views
Issue with samtools reheader, bam file
samtools chromosome BAM reheader notation
updated 4.1 years ago by ★ 3.0k • written 4.2 years ago by ▴ 10
0
votes
0
replies
1.1k
views
Error in cvr.glmnet(): formal argument "x" matched by multiple actual arguments
LASSO glmnet R ipflasso
4.2 years ago by lluc.cabus ▴ 30
2
votes
4
replies
5.5k
views
BAM File, Change chromosome notation
samtools chromosome header BAM notation
updated 4.2 years ago by ★ 3.0k • written 4.2 years ago by ▴ 10
0
votes
2
replies
990
views
Intra-dataset (Single Dataset) Batch Correction Tips for scRNA-seq
scrna-seq batch-effect-correction
4.2 years ago by ksaunders73 ▴ 10
0
votes
3
replies
1.2k
views
strand-specific RNA-seq analysis
RNA-seq lncRNA mRNA
updated 4.1 years ago by ★ 1.3k • written 4.2 years ago by ▴ 30
0
votes
0
replies
652
views
chip seq data .narrow dataset
TF narrow from intensity chip
updated 4.2 years ago by 153k • written 4.2 years ago by ▴ 70
7
votes
6
replies
2.7k
views
What is the best practice for analysing single-cell data with low sequencing depth?
10X depth scRNA-seq Sequencing Seurat data
4.2 years ago by VolEr ▴ 40
1
vote
1
reply
712
views
Ranking treatment replicates from differential expression
differential expression
updated 4.2 years ago by ★ 3.1k • written 4.2 years ago by ▴ 80
0
votes
2
replies
1.1k
views
Linear versus affine gap cost
affine linear cost Alignment gap
4.2 years ago by rtho ▴ 20
121,831 results • Page 614 of 2437
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Comment: Parabricks : Number of GPUs requested (2) is more than number of GPUs (0) in the by Pierre Lindenbaum 166k
@genomax I'm using the 'GPU' queue of my cluster (SLURM). The very same config was used with another parabrick subtool and I got not probl…
Comment: Parabricks : Number of GPUs requested (2) is more than number of GPUs (0) in the by GenoMax 153k
Are you running this under a job scheduler? Is there a separate partition for the GPU's/are they accessible to the scheduler?
Comment: Learning Bioinformatics doing Projects by Anjali • 0
thank you.
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Are the batches biological replicates?
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If you want to save time at the cost of having a lesser understanding of how bioinformatic programs work, you may study through the BioStar…
Answer: how to start by shelkmike ★ 1.7k
I would recommend, in the following order:<br> 1) Go through Bioinformatics Algorithms, either as a video course or as a book, and do all e…
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For what is worth, in a previous project, I have done some tests on different hierarchical clustering methods for single cell RNAseq. I had…
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* Get some data - either your own or from a paper / GEO / ArrayExpress / SRA / TCGA / cBioPortal etc etc. * Look at the methods of papers…
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"ward.D2" -- top of the pops in terms of interpretatble clusters from gene expression data in my hands, the rest is...often crytpic.
Comment: High percentage of intronic/intergenic reads in RNA-seq by i.sudbery 22k
I'd expect to see more or less what they see in your reference. Somewhere between half and two thirds of reads mapping to exons. The low fr…
Comment: Perform Hierarchical Clustering in R with ggdendro Visualization by Bastien Hervé 6.4k
As the whole presentation relies on a distance matrix and elements aggregation by hierarchical clustering, it would be helpful to better un…
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> Read in data Add an example of what is in `data.csv`.
Comment: How to submit a bacterial (endosymbiont) ITS rDNA sequence to GenBank? by GenoMax 153k
That is unfortunate. Perhaps try one more time to see if you can reach a more considerate help desk person with this try. In dealings with …
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Yes, I tried asking support for help, but I received a rude response. I was too embarrassed to ask again.
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Were https://www.genewiz.com/ and/or Novogene https://www.novogene.com/ on your list already? Several university sequencing core labs may a…
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