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News: Online training - Genomic Prediction
Genomics
4.1 years ago by Physalia-courses ★ 2.7k
1
vote
2
replies
1.1k
views
Plotting chromosomes and target capture baits
plotting target_capture Hyb-Seq R
4.1 years ago by Begonia_pavonina ▴ 210
1
vote
1
reply
775
views
Problem of visualizing results of PPI network
analyst network Cytoscape
updated 4.1 years ago by ▴ 310 • written 4.1 years ago by ▴ 20
0
votes
0
replies
666
views
Cutoffs for Proxy Identification: D' and R^2
plink2
4.1 years ago by dec986 ▴ 380
5
votes
15
replies
4.4k
views
7 follow
DESeq2 normalization - Found Difference in values when calculated manually
DESeq2 normalization difference
4.1 years ago by Sandhiya ▴ 20
0
votes
1
reply
994
views
getting different value list from GATK gc content and CANOES
CNV GATK CANOES
updated 4.1 years ago by • 0 • written 6.2 years ago by • 0
0
votes
1
reply
895
views
How is better perform the analyze the somatic mutations? (the mutations of my interest gene)
somatic VCF annotation Oncoplot
updated 4.1 years ago by ★ 3.0k • written 4.1 years ago by • 0
1
vote
1
reply
962
views
How to load user-defined genome in IGV-webapp
IGV-WEBAPP IGV igv
updated 4.1 years ago by 154k • written 4.1 years ago by ▴ 60
2
votes
6
replies
1.9k
views
Statistics on RNAseq data
on Statistics data RNAseq
updated 4.1 years ago by ▴ 350 • written 4.1 years ago by ▴ 30
0
votes
0
replies
886
views
Job: Bioinformatics position at the spatial transcriptomics facility of Lyon (France)
single-cell spatial-transcriptomics
updated 2.9 years ago by 45k • written 4.1 years ago by • 0
1
vote
2
replies
1.4k
views
Error when opening CEL files in python
python
updated 4.1 years ago by ★ 1.6k • written 4.1 years ago by • 0
1
vote
2
replies
1.3k
views
Variant Allele Frequency
Cancer
updated 4.1 years ago by ★ 3.0k • written 4.1 years ago by ▴ 60
0
votes
4
replies
2.3k
views
Find NLS in list of proteins.
localization nuclear signal
updated 4.1 years ago by 22k • written 4.1 years ago by ▴ 60
1
vote
4
replies
1.6k
views
Multiple hypothesis correction with multiple gene sets
gene-set-enrichment GO multiple-test-correction GO-enrichment
updated 4.1 years ago by ★ 8.3k • written 4.1 years ago by • 0
0
votes
2
replies
1.7k
views
HRD score LST?
cnv
updated 4.1 years ago by ★ 1.1k • written 5.0 years ago by ▴ 90
2
votes
2
replies
1.1k
views
Sudden coverage increase in IGV
IGV sequencing coverage
updated 4.1 years ago by • 0 • written 4.1 years ago by • 0
1
vote
2
replies
1.3k
views
How to get all genes and their annotations within a LD block?
GWAS haplotype SNPs genome wheat Ensembl
4.1 years ago by b.g.tamang ▴ 20
0
votes
2
replies
3.8k
views
From Bismark to methylkit, which file is better to use?
Bisulfite sequencing Bismark methylkit
updated 12 months ago by ★ 1.2k • written 4.9 years ago by ▴ 130
0
votes
1
reply
738
views
Regarding functional similarity analysis by GOSemSim package of R
GOSemSim
updated 4.1 years ago by 27k • written 4.1 years ago by • 0
0
votes
2
replies
1.9k
views
trinity run_DE_analysis.pl Failed with error: ‘package ‘limma’ could not be loaded’
run_DE_analysis.pl trinity
4.1 years ago by Rajesh ▴ 10
2
votes
4
replies
2.3k
views
Any suggestion on metagenomics pipelines for processing shotgun metagenomics whole genome sequencing samples?
metagenomics_pipelines WGS shotgun_metagenomics antimicrobial_resistance
4.1 years ago by eli_bayat ▴ 100
1
vote
3
replies
2.1k
views
WGCNA
Installation WGCNA
updated 4.1 years ago by ▴ 940 • written 4.1 years ago by ▴ 10
0
votes
0
replies
652
views
Neighboring index between clusters on a map
connectivity clustering
4.1 years ago by thejustpark ▴ 80
2
votes
3
replies
2.4k
views
GIAB Benchmark (High Confidence) Bed Filles
SNPS GIAB variants
updated 4.1 years ago by ▴ 290 • written 4.1 years ago by ▴ 840
8
votes
10
replies
5.2k
views
UCSC knownCanonical hg19 vs. hg38
genome UCSC hg19 hg38 canonical
updated 4.1 years ago by ▴ 670 • written 4.6 years ago by ▴ 150
1
vote
2
replies
1.4k
views
Tool: krust: a k-mer counter in Rust using the rust-bio and rayon crates
Rust kmer-counting fasta kmer
updated 4.1 years ago by 103k • written 4.1 years ago by ▴ 10
0
votes
2
replies
1.0k
views
Can i estimate the hormone-receptor binding affinity ?
hormone
updated 2.6 years ago by 45k • written 4.1 years ago by • 0
1
vote
2
replies
1.0k
views
Edit vcf file 0|0 to 0
linux vcf genomics edit
4.1 years ago by zoubda • 0
2
votes
4
replies
2.0k
views
Problem with BAM file headers
SAM GATK BAM
4.1 years ago by Lucas • 0
0
votes
0
replies
875
views
Weird PCA plot using WGCNA results
cancer PCA expression WGCNA plot
4.1 years ago by seta ★ 1.9k
0
votes
1
reply
1.2k
views
List of codon numbers in a panel
browser codon list ucsc genome
updated 4.1 years ago by ▴ 670 • written 4.5 years ago by • 0
2
votes
6
replies
4.5k
views
GenomeInfoDb (in R) and UCSC just stopped co-operating in terms of mm10
seqlevels seqlevelsStyle GenomeInfoDnb R UCSC
updated 4.1 years ago by 36k • written 4.3 years ago by ▴ 20
1
vote
3
replies
2.5k
views
clusterProfiler: number of GO terms in results
clusterProfiler
4.1 years ago by thistleq777 ▴ 10
2
votes
2
replies
1.9k
views
PRSice-2 without Ref SNP ID
Catalog PGS PRSice PRS
4.1 years ago by Jenish ▴ 20
0
votes
0
replies
563
views
How to do virtual screening and determining pharmacore
QSAR Docking
4.1 years ago by ashwing.kofficial ▴ 10
8
votes
3
replies
4.2k
views
Please help me understand linkage disequilibrium
LD Linkage disequilibrium SNP
updated 4.1 years ago by 22k • written 4.1 years ago by ▴ 60
0
votes
0
replies
1.2k
views
Job: PhD student for a computational breast cancer research project
Cancer PhD Omics
updated 2.7 years ago by 45k • written 4.1 years ago by • 0
1
vote
1
reply
2.2k
views
Ensembl VEP Docker: cannot write to FASTA lockfile
Ensembl Docker VEP
updated 4.1 years ago by 24k • written 4.1 years ago by • 0
0
votes
0
replies
756
views
How to show intermolecular forces between two chains within the same protein in Pymol
protein python pymol antibody antigen
4.1 years ago by Lucy • 0
2
votes
2
replies
1.5k
views
network analysis for microbial amplicon sequencing data
plot Network igraph R
4.1 years ago by Bioinfonext ▴ 480
0
votes
2
replies
1.6k
views
Unicycler and GNU parallel
Unicycler parallel
4.1 years ago by emma.a ▴ 130
0
votes
1
reply
3.1k
views
PROVEAN input script
python provean variant effect prediction
updated 4.1 years ago by • 0 • written 8.1 years ago by ▴ 10
0
votes
0
replies
706
views
GREAT genome ontology top hits criteria?
bed GREAT gene-ontology go
updated 2.7 years ago by 45k • written 4.1 years ago by ▴ 40
0
votes
0
replies
682
views
Job: Postdoctoral Scientist in Statistical Bioinformatics and Software Development, WEHI, Melbourne, Australia
Australia
4.1 years ago by Gordon Smyth ★ 8.3k
0
votes
0
replies
845
views
GREAT difference between 'mouse phenotype' and 'mouse phenotype single KO'
bed gene-ontology GREAT go
updated 2.7 years ago by 45k • written 4.1 years ago by ▴ 40
0
votes
1
reply
1.0k
views
Running htseq-count to "grab" long non coding gene_id names
lncRNA htseq
updated 4.1 years ago by 154k • written 4.1 years ago by ▴ 210
3
votes
3
replies
1.4k
views
Germline Cancer Mutations
Cancer
updated 4.1 years ago by 4.2k • written 4.1 years ago by ▴ 60
198
votes
46
replies
77k
views
34 follow
Tutorial: Analysing Microarray Data In Bioconductor
microarray-analysis bioconductor
updated 7 months ago by • 0 • written 13.1 years ago by 20k
0
votes
0
replies
725
views
Has anybody used RIP-MD tool for generation of RIN from MD trajectories?
Interaction MD simulation VMD Network Residue
4.1 years ago by Anjali • 0
12
votes
5
replies
2.0k
views
Remove duplicates in fasta files based on a specific value with awk
sort fasta sed awk
updated 4.1 years ago by 21k • written 4.1 years ago by ▴ 30
122,027 results • Page 582 of 2441
Recent Votes
A: What does BAF mean?
What does BAF mean?
Comment: VCF: Replacing RefSeq ID to chr in #CHROM
A: VCF: Replacing RefSeq ID to chr in #CHROM
Answer: Modeling/simulations using SNPs data
what is the output of 'samtools coverage'
Answer: Discrepancy in Q-score assessment of ONT reads in Nanopore and third-party softw
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Comment: Brave: Bioinformatics Reactive Analysis and Visualization Engine by Edward • 0
Thanks for the reply and suggestions. This software is a bit similar to galaxy. Recently, I am adding an application store for pipelines, s…
Answer: Modeling/simulations using SNPs data by Dave Carlson ★ 2.2k
I would recommend looking into using [SLiM][1] for forward-time population genetic simulations. It's widely used and very well documented, …
Answer: Strugling on the 3'rule of HGVS by Jeremy Leipzig 23k
> chrM : m.57T>TC, but according to the 3'rule it should be named m.60T>TC (if I understood correctly). no that cannot be shifted, like yo…
Answer: Extract fastq sequences based on date/time (which is in the header) by zhanxw ▴ 20
This tool can be helpful: https://github.com/angelovangel/nanotimes
Answer: Filter nanopore fastq files by start time by zhanxw ▴ 20
This is an efficient tool: https://github.com/angelovangel/nanotimes
Answer: Choosing enrichment analysis tool by i.sudbery 22k
Standard enrichement tools, like Metascape, Enrichr or David assume that under a model of no pathway being particularly involved in what yo…
Answer: Discrepancy in Q-score assessment of ONT reads in Nanopore and third-party softw by k-tarasov ▴ 10
Thanks to colindaven answer, I managed to travel by hyperlinks to the source of the discrepancy. It seems that Nanopore tools compute *ave…
Answer: Discrepancy in Q-score assessment of ONT reads in Nanopore and third-party softw by colindaven 8.0k
I agree completely. I think the cause is well discussed here : https://github.com/OpenGene/fastplong/issues/20 `fastplong` currently sti…
Comment: Discrepancy in Q-score assessment of ONT reads in Nanopore and third-party softw by k-tarasov ▴ 10
Thank you for answer. No, I am looking at all reads before appllying any filters. There are 2,429,312 raw reads, and in 16s-wf pipeline I …
Comment: Discrepancy in Q-score assessment of ONT reads in Nanopore and third-party softw by GenoMax 154k
Are you only looking at reads that satisfy this filter (which is in your command line in GitHub post) in your `seqkit` and `fastqc` reports…
Comment: Configuration file for DSP WTA by GenoMax 154k
> data starting from Fastq Generally did this with the entire flowcell folder and not fastq files. The data needs to be demultiplexed in a…
Answer: How to create a consensus of a contig with samtools or bbmap? by jkbonfield ★ 1.3k
Your first command outputted SAM rather than BAM, and SAM without a header (no `-h`) option. If you used `-o contig_1.bam` it would have w…
Comment: Brave: Bioinformatics Reactive Analysis and Visualization Engine by ATpoint 89k
Seconding this, I also felt completely lost what this actually does. @OP, you need to learn to make sharp, concise bulletpoints advertising…
Answer: Validating snRNA-seq cell type by correlating with other datasets by ATpoint 89k
I would not do correlation analysis like this, I don't see how this makes any sense. Integration is possible but cumbersome. Instead, use `…
Comment: Choosing enrichment analysis tool by Marlene • 0
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