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How to calculate/visualize network robustness/vulnerability?
Erdos-Renyi Barabasi-Albert igraph
3.2 years ago by english.server ▴ 300
0
votes
4
replies
2.2k
views
Missing genes in converting "ensembl_gene_id_version" to "ensembl_gene_id" in biomaRt package
genes biomaRt R
3.2 years ago by Maryam • 0
0
votes
0
replies
614
views
Nucleotide codes - gap vs low quality basecalls
assembly ncbi gap basecall nucleotide
3.2 years ago by timothy.kirkwood ▴ 140
1
vote
1
reply
1.2k
views
Calculating bootstrap for psmc
psmc
updated 3.2 years ago by ▴ 10 • written 3.7 years ago by ▴ 350
0
votes
0
replies
669
views
News: ONLINE COURSE - RADseq data analysis using Stacks
Phylogenomics Population RADseq Genomics Stacks
3.1 years ago by Physalia-courses ★ 2.6k
0
votes
1
reply
710
views
Can i restart gatk GenomicsDBimport?
gatk GenomicsDBimport restart
updated 4 months ago by ▴ 20 • written 3.2 years ago by • 0
1
vote
0
replies
860
views
Job: Bioinformatics Officer - South Australian Genomics Centre (SAGC)
genomics
updated 2.4 years ago by 45k • written 3.2 years ago by ▴ 50
0
votes
1
reply
622
views
I have two different libaries which were sequenced, How should I compare their library diversity?
bam sam
updated 2.3 years ago by 45k • written 3.2 years ago by ▴ 40
0
votes
0
replies
569
views
Bar and line graphs using Bokeh Module in python
Plots Biopython
updated 3.1 years ago by 45k • written 3.2 years ago by ▴ 140
0
votes
2
replies
1.4k
views
how to split a Bam by chromosome and unplaced scaffolds.
samtools bam
updated 2.1 years ago by 45k • written 3.2 years ago by ▴ 50
1
vote
3
replies
1.4k
views
Genotypic and clinical phenotypic feature selection methods for machine learning (in python)?
python machine-learning
updated 3.2 years ago by ★ 29k • written 3.2 years ago by ▴ 50
0
votes
5
replies
2.0k
views
PHATE in R cannot detect matplotlib python dependency but numpy is fine
PHATE
3.2 years ago by abhay.kanodia ▴ 10
0
votes
0
replies
560
views
16S (18S) rRNA primer design
taxonomy primer design mopo16s
3.2 years ago by noodle ▴ 650
1
vote
2
replies
4.9k
views
How to generate plink map files
plink gwas
updated 3.2 years ago by 11k • written 3.2 years ago by ▴ 50
0
votes
9
replies
2.0k
views
BlastX through Biopython
Biopython
updated 3.1 years ago by 45k • written 3.2 years ago by ▴ 140
0
votes
1
reply
862
views
how to download NCBI partially non-redundant nucleotide dataset for prokaryotes?
NCBI prokaryote
updated 2.3 years ago by 45k • written 3.2 years ago by ▴ 180
0
votes
2
replies
856
views
Normalization of Counts Matrix
Expression Normalization Differential Counts
3.2 years ago by kdhp20607 • 0
0
votes
0
replies
562
views
Using PLINK for (ROH) analysis using full genome
map ped vcf roh plink
updated 3.2 years ago by 152k • written 3.2 years ago by ▴ 20
16
votes
5
replies
14k
views
6 follow
Tutorial: Easy way to do GO enrichment in R
enrichr RNA-Seq gene R
updated 2.3 years ago by 45k • written 7.6 years ago by ▴ 800
4
votes
1
reply
822
views
Cancer-cell-line-specific essential genes
genes database essential
updated 3.2 years ago by 89k • written 3.2 years ago by ▴ 300
0
votes
0
replies
461
views
scRNA-seq and Tumor heterogeneity for better cancer insights?
single-cell-rna Cancer
updated 3.1 years ago by 45k • written 3.2 years ago by • 0
1
vote
2
replies
1.2k
views
GENECODE gene annotation and ENSEMBL annotation analogy
ensembl gencode
3.2 years ago by tsomakiank ▴ 50
0
votes
2
replies
1.1k
views
clusterprofiler gsea analysis
clusterprofiler gsea organism
updated 3.2 years ago by 21k • written 3.2 years ago by ▴ 60
0
votes
1
reply
653
views
Bacterial whole genome pathway analysis
pathway kegg R
updated 3.2 years ago by ★ 29k • written 3.2 years ago by • 0
0
votes
0
replies
1.0k
views
Python assistance -ete3
etetoolkit
updated 2.1 years ago by 45k • written 3.2 years ago by • 0
5
votes
5
replies
1.6k
views
A first trial in machine learning for a classification problem: data set up and logic
caret MachineLearning R classifier
updated 3.2 years ago by ▴ 930 • written 3.2 years ago by ▴ 100
0
votes
2
replies
917
views
Problem in getting SNAI1 gene in prostate DEG table
TCGAbiolinks SNAI1gene ProstateDEG
3.2 years ago by Maryam • 0
3
votes
10
replies
5.1k
views
TMM or TPM for RNA sequence differential gene expression analysis
TPM DGEA sequence RNA TMM
updated 3.2 years ago by 102k • written 3.2 years ago by • 0
2
votes
5
replies
1.8k
views
Problem on R when creating a PCA plot
ggfortify R PCA
updated 2.2 years ago by 45k • written 3.2 years ago by ▴ 10
2
votes
4
replies
1.2k
views
Microorganisms source isolation
bacteria NCBI taxonomy metadata isolation
3.2 years ago by Giulia.cosenza ▴ 110
2
votes
1
reply
579
views
Strange peak in gene coverage plot (MultiQC)
QC genebody_coverage RNA-seq pico SMARTer
updated 3.2 years ago by 152k • written 3.2 years ago by ▴ 10
1
vote
4
replies
1.4k
views
trimming a paired end sra
adapter fastqc rna-seq
updated 3.2 years ago by 152k • written 3.2 years ago by ▴ 60
4
votes
2
replies
9.4k
views
outfmt 6 BLAST column names
outfmt6 blast output
updated 3.2 years ago by 152k • written 3.2 years ago by ▴ 60
13
votes
8
replies
2.6k
views
6 follow
paired end mapping with one end being unique and the other end multiple
paired-end genome ngs
updated 2.7 years ago by ★ 3.0k • written 3.2 years ago by • 0
6
votes
3
replies
1.0k
views
Seeking a platform like R language for NGS data manipulation
NGS R data analysis
3.2 years ago by field654 ▴ 30
4
votes
7
replies
1.8k
views
why exon and intergenic region overlap
intergenic exons region
3.2 years ago by Binghong ▴ 20
0
votes
1
reply
981
views
Limma false positives
limma metabolomics
updated 3.2 years ago by ★ 8.2k • written 3.2 years ago by • 0
1
vote
2
replies
1.7k
views
How to perform VST on my filtered counts data
RNA-seq transformation VST
updated 3.2 years ago by 15k • written 3.2 years ago by ▴ 170
4
votes
1
reply
724
views
Comparing several prognosis scores
survival prognosis
updated 3.2 years ago by ▴ 930 • written 3.2 years ago by ▴ 20
0
votes
0
replies
685
views
How to download phastcons and phyloP scores of great ape genome
Conservation
3.2 years ago by Joe ▴ 40
0
votes
0
replies
514
views
How to have Bio.Blast NCBIWWW return an .xml file to my hard disk
Biopython
3.2 years ago by mfeather • 0
0
votes
0
replies
702
views
Get reference genome from Kraken2 taxID
metagenome kraken2
3.2 years ago by schmiggle • 0
1
vote
2
replies
1.7k
views
Normalization of RNA-Seq Counts with ERCC spike-ins
TPM ERCC fpkm normalization RNA-Seq
updated 3.2 years ago by ★ 1.9k • written 3.2 years ago by • 0
0
votes
6
replies
1.7k
views
Command line BLAST is very slow
blastp BLAST blast blastn
updated 3.2 years ago by 152k • written 3.2 years ago by • 0
1
vote
0
replies
618
views
MSA: Gene Family annotation
Analysis Multiple Sequence Genome-Wide Alignment MAPKKK
3.2 years ago by Dillon ▴ 10
2
votes
2
replies
1.1k
views
Adding to 10X genome.fa and genes.gtf files
10x Genomics multiome scRNA-seq
3.2 years ago by rbronste ▴ 420
0
votes
0
replies
1.3k
views
Modified Basecalling with Guppy
Alignment Guppy
3.2 years ago by Azlan • 0
0
votes
1
reply
1.0k
views
SortMeRNA for multiple samples--how to stop overwriting
RNAseq sortmerna
updated 2.8 years ago by • 0 • written 3.2 years ago by • 0
0
votes
0
replies
642
views
R package PopGenome : error with introgression.stats function
PopGenome R
updated 2.3 years ago by 45k • written 3.2 years ago by • 0
1
vote
5
replies
1.9k
views
Get GO terms for location and filter protein table with Rstudio
Rstudio location GOterms transmembrane GOdatabase
updated 3.2 years ago by 3.3k • written 3.2 years ago by • 0
121,523 results • Page 429 of 2431
Recent Votes
Answer: NCBI Datasets CLI Question
Answer: NCBI Datasets CLI Question
Comment: PacBio amplicon reads partially aligned using minimap2 – library or analysis iss
Comment: PacBio amplicon reads partially aligned using minimap2 – library or analysis iss
Answer: NCBI Datasets CLI Question
SNP calling with SAMtools on multiple samples
Comment: Crac: Funny And/Or Weird Names For Bioinformatics Tools
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Recent Replies
Comment: NCBI Datasets CLI Question by Bjorn • 0
Thanks! Works great.
Comment: PacBio amplicon reads partially aligned using minimap2 – library or analysis iss by louisflower1999 • 0
Hi GenoMax, Thanks so much for your suggestion! Those amplicons are around 4.4kb. And there should be at least 1kb from the left and 800 b…
Comment: NCBI Datasets CLI Question by GenoMax 152k
Wanted to make it a complete answer with an additional command. Moved now.
Comment: NCBI Datasets CLI Question by Mensur Dlakic ★ 29k
Maybe make this an answer rather than a comment?
Comment: PCA interpretation by swbarnes2 15k
You are trying to PCA these by what, exactly? Binned coverage? Is this really informative?
Answer: NCBI Datasets CLI Question by GenoMax 152k
I don't see a way to specify a random number of accessions to download as an option. Perhaps you may want to open an issue and suggest that…
Comment: PacBio amplicon reads partially aligned using minimap2 – library or analysis iss by Zev.Kronenberg 12k
@genomax has a good point about trying `pbaa`. The tool will output consensus sequences of the different alleles. You can then use MSA to a…
Answer: Joint Calling for Large Germline WGS Cohort by Jeremy Leipzig 23k
Not to get too pedantic but joint genotyping solves a different problem (removing artefactual variants) from producing a population VCF tha…
Answer: Joint Calling for Large Germline WGS Cohort by DBScan ▴ 490
Another option would be HAILs VDS Combiner, [https://hail.is/docs/0.2/vds/hail.vds.combiner.VariantDatasetCombiner.html#hail.vds.combiner.V…
Comment: how shoud the phred score be intepreted? by QX ▴ 70
thank you for explanation and documentation
Comment: how shoud the phred score be intepreted? by GenoMax 152k
Illumina sequencing assumes/generally expects that clusters in a sequencing field have an even distribution of ACTG so for every sequencing…
Comment: how shoud the phred score be intepreted? by QX ▴ 70
what do you mean by 'low nucleotide diversity'. If it is low nucleotide diversity, is it supposed to have consistent signals, leading to hi…
Answer: how shoud the phred score be intepreted? by GenoMax 152k
> Does the phred-score is affected by the position of the base in all the reads (vertical), or all the bases that belong to a single read (…
Answer: Joint Calling for Large Germline WGS Cohort by Pierre Lindenbaum 166k
try glnexus https://github.com/dnanexus-rnd/GLnexus/wiki/Getting-Started
Comment: Inherited pipeline uses RNA-seq variant calls for WASP filtering—shouldn’t it be by jonas.andersson ▴ 40
Thank you so much for you answer @iansudbery! Yes I have read it too and I don't think it's totally clear either, so I guess I might not be…
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