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122,201 results • Page 610 of 2445
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6
votes
7
replies
5.4k
views
Biopython SeqIO: AttributeError: 'str' object has no attribute 'id'
filtering biopython fasta python sequence
updated 4.3 years ago by ★ 1.6k • written 4.3 years ago by ▴ 10
0
votes
2
replies
1.2k
views
Plot assigned / unassigned reads distance to 3'UTR
bedtools RNA-seq closest
4.3 years ago by nlehmann ▴ 150
2
votes
4
replies
2.5k
views
How to compare LD of a gene for all subpopulations in 1000 Genome?
LDPlot SNPs variants 1000Genome
4.3 years ago by Rashmi ▴ 20
3
votes
11
replies
7.9k
views
Converting gene symbols to protein (uniprot) ids gives multiple matches per gene symbol. Why?
Uniprot r
updated 4.3 years ago by 21k • written 4.4 years ago by ▴ 60
0
votes
0
replies
1.1k
views
manhattan plot
fst vcf manhattan
4.3 years ago by anithanagaraj93 ▴ 10
4
votes
6
replies
1.9k
views
Genome analysis and improvement
genome
4.3 years ago by Duminda ▴ 10
0
votes
4
replies
3.5k
views
How to modify dot plot in MUMmer 3 for bacteria comparative genomics?
mummerplot
updated 4.3 years ago by ★ 30k • written 4.3 years ago by ▴ 30
4
votes
4
replies
1.8k
views
Exonerate - issues when running it
Exonerate
4.3 years ago by helloword • 0
0
votes
1
reply
874
views
Using FPKM value from the database
gene-expression FPKM
updated 4.3 years ago by 45k • written 4.3 years ago by ▴ 40
0
votes
5
replies
3.9k
views
CellPhoneDB results
CellPhoneDB statistics
4.3 years ago by torabian.p • 0
0
votes
0
replies
756
views
How can I find genomes that have linked transcriptome data ? (bacteria)
bacteria esearch ncbi
4.3 years ago by hugo.avila ▴ 540
4
votes
4
replies
2.2k
views
Extract subject sequences from Blast result
sequence blast homology
4.3 years ago by mnsp088 ▴ 100
0
votes
0
replies
788
views
GSEA p value dependent on pre-ranked list size?
gsea enrichment p-value statistics
4.3 years ago by garfield320 ▴ 20
0
votes
0
replies
783
views
Job: Need bioinformatician at UCSF to study infectious disease & malaria genomic epidemiology & serology
bioinformatician
updated 2.5 years ago by 45k • written 4.3 years ago by • 0
6
votes
4
replies
6.9k
views
Pandas dataframe to H5ad file
H5 python pandas
4.3 years ago by roy.granit ▴ 890
0
votes
3
replies
1.9k
views
Missing mappability file for mm10
mm10 mappability
updated 4.3 years ago by 45k • written 6.4 years ago by ▴ 20
0
votes
1
reply
2.8k
views
Clusterprofiler object 'GO2ONT' not found
get_GO_data go2ont enrichgo clusterprofiler GO
4.3 years ago by corinne_hutfilz • 0
0
votes
3
replies
1.6k
views
CreatePHG_step2_consensu
PHGwiki PHG
updated 4.3 years ago by ▴ 220 • written 4.3 years ago by • 0
0
votes
0
replies
446
views
Can´t create a consensus file from my VCF and reference genome
migrate-n
4.3 years ago by Dieggar • 0
1
vote
4
replies
2.3k
views
R package for filtering expression data
gene-expression r EMA
updated 4.3 years ago by 45k • written 4.3 years ago by ▴ 70
0
votes
1
reply
1.1k
views
ARACNE Minet R studio
ARACNE Minet
updated 4.3 years ago by 3.9k • written 4.3 years ago by • 0
0
votes
2
replies
1.1k
views
Should I run GISTIC2.0 for cases/controls separately?
GISTIC2.0 CNV CNA
updated 4.3 years ago by 45k • written 4.3 years ago by • 0
0
votes
1
reply
646
views
Problem for interpreting results of ClusterViz
Cytoscape
updated 4.3 years ago by ▴ 310 • written 4.4 years ago by ▴ 20
0
votes
1
reply
818
views
Cytoscape - How to filter when starting from a complete network, built from a gene-to-gene adjacency matrix
cytoscape
updated 4.3 years ago by ▴ 310 • written 4.4 years ago by ▴ 30
0
votes
1
reply
637
views
Cytoscape: GeneMANIA plug-in output.
GeneMANIA analysis cytoscape network analysis.
updated 4.3 years ago by ▴ 310 • written 4.4 years ago by • 0
2
votes
2
replies
1.4k
views
How to use RINalyzer plugin in cytoscape
cytoscape RINalyzer networks
updated 4.3 years ago by ▴ 310 • written 4.4 years ago by ▴ 940
2
votes
3
replies
2.1k
views
How to plot/combine biological replicates on a genomic features plot for methylated array?
array methylation beadchip plot features genomic
updated 4.3 years ago by ★ 3.1k • written 4.3 years ago by ★ 1.1k
10
votes
8
replies
8.4k
views
Bcftools how to add DP to FORMAT field (get per sample read depth for REF vs ALT alleles )
bcftools snp vcf calling
updated 4.3 years ago by ▴ 140 • written 4.4 years ago by ▴ 80
11
votes
13
replies
4.2k
views
Why is WGS/WES depth of Y chromosome highly variable?
chromosome-Y whole-genome-sequencing
updated 2.9 years ago by 45k • written 4.3 years ago by ▴ 270
3
votes
7
replies
2.8k
views
How to infer segment direction from vcf
SV vcf NGS
4.3 years ago by octpus616 ▴ 120
0
votes
0
replies
1.3k
views
Explanation of generatio from clusterProfiler package
transcriptomic proteomics
4.3 years ago by javanokendo ▴ 60
2
votes
5
replies
2.7k
views
Reference file for base recalibration
base NGS recalibration preprocessing GATK
4.3 years ago by priya.bmg ▴ 70
5
votes
2
replies
2.8k
views
Calculating minor allele frequency for GnomAD VCF file
gnomAD genome
updated 4.3 years ago by ▴ 50 • written 5.0 years ago by ▴ 20
8
votes
5
replies
6.1k
views
Quickly get allele frequencies from Gnomad
gnomad allele freq ngs
updated 3.1 years ago by ▴ 50 • written 5.3 years ago by ▴ 170
4
votes
10
replies
3.7k
views
Help With TCGAbiolinks package
rnaseq TCGA tcgabiolinks R bioconductor
4.3 years ago by daniela.paola.s.p ▴ 70
0
votes
4
replies
2.0k
views
How to convert gene names to EC numbers?
database
updated 4.3 years ago by 16k • written 4.3 years ago by ▴ 250
4
votes
3
replies
2.5k
views
RNA-Seq Mapping Genome or Transcriptome
Genome Transcriptome Rna-Seq
updated 4.3 years ago by ▴ 90 • written 4.3 years ago by ▴ 40
1
vote
0
replies
903
views
Tool: Omics Playground: visualization and analysis of transcriptomics and proteomics data
proteomics RNA RNA-seq scRNA-seq omics data
4.3 years ago by bigomics.team ▴ 90
0
votes
0
replies
668
views
Biotype assignment for co-expression network
biotype co-expression
4.3 years ago by imaparna27 ▴ 20
2
votes
5
replies
4.5k
views
collapsing pacbio reads into a single sequence
pacbio
4.3 years ago by Sara ▴ 280
0
votes
0
replies
969
views
News: Online training -Metabolomics in R
Metabolomics
4.3 years ago by Physalia-courses ★ 2.7k
0
votes
1
reply
1.1k
views
Older version of markers from Chocophlan
Chocophlan Metaphlan
updated 4.3 years ago by 45k • written 4.3 years ago by ▴ 70
2
votes
2
replies
1.7k
views
Mark Duplicates
picard GATK NGS
4.3 years ago by priya.bmg ▴ 70
0
votes
0
replies
675
views
GenomicRatioSet object after minfi normalization does not show method used for preprocessing.
Illumina minfi EPIC R
4.3 years ago by samuel.carleial • 0
0
votes
0
replies
1.2k
views
How to interpret scRNA-Seq cell dynamics from scVelo and CytoTrace results
velocyto cell cytotrace rnaseq dynamics
4.3 years ago by gundalav ▴ 380
1
vote
2
replies
10k
views
TypeError: must be real number, not dict in python
string python dict
updated 4.3 years ago by 22k • written 4.3 years ago by • 0
3
votes
2
replies
1.7k
views
What cut-offs to use for Genomic Features Pie Chart for Methylation Array Data?
beadchip array methylation
4.3 years ago by Pratik ★ 1.1k
3
votes
4
replies
1.8k
views
How many reads does Delly use for variant calling?
DNA-seq bwa-mem delly bowtie2
updated 3.6 years ago by ▴ 10 • written 4.3 years ago by ▴ 30
2
votes
1
reply
2.4k
views
How to filter delly variants?
calling DNA-seq delly variants
updated 4.3 years ago by ★ 2.0k • written 4.3 years ago by ▴ 30
0
votes
1
reply
755
views
Finding Molecular function for more than 100 GO terms
Gene Ontology
updated 4.3 years ago by 166k • written 4.3 years ago by ▴ 20
122,201 results • Page 610 of 2445
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strong appearing variant not found by haplotypecaller in -ERC mode and deepvariant but with haplotypecaller in normal mode
Answer: How can I easily remove overlapping transcripts, keeping only longest transcript
Answer: Log2 transformation is well used, but is there a good paper that can be used as
Answer: Flatten a GTF
Answer: RNA-seq - Creating SAF from NCBI gff for Subread featureCounts - keep 'gene' or
Can EdgeR of DeSeq be used for Single-cell RNA-seq?
Answer: Getting the overlap between two GTF files
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Recent Replies
Comment: ID unifiying across different datasets by GenoMax 154k
Each database has their own method of annotation/validation. Depending on resources available there may be a lag between the databases in t…
Comment: low quality data or file name swapping -- cellranger arc errors when processing by Wu-Sheng Zhang • 0
Hi @arup , thank you very much for your suggestions, and here are the results -- they seems correct. May I have your suggestions? Thank you…
Comment: Why did the QV value decrease significantly after using YAHS for HiC scaffolding by samuel.a.odonnell ▴ 640
I don't believe merqury ignores softmasked (lower case) nucleotides so I don't think that is the case. From what it sounds like, during th…
Comment: ID unifiying across different datasets by zizigolu ★ 4.4k
Thanks a lot to be helpful I’m trying to build a complete `UniProtID` to `GeneSymbol` lookup table and I’m running into a wall. I’ve alrea…
Comment: strong appearing variant not found by haplotypecaller in -ERC mode and deepvaria by thomas.heigl.ibk ▴ 20
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 ▴ 20
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)?
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