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122,008 results • Page 273 of 2441
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Ballgown
Ballgown differential-expression-analysis R
updated 2.5 years ago by 45k • written 2.5 years ago by • 0
0
votes
1
reply
2.5k
views
Cannot install limma
bioconductor limma
updated 2.5 years ago by ▴ 660 • written 2.5 years ago by ▴ 170
0
votes
9
replies
1.5k
views
User's choice for three- or single- letter amino acids in reading frames
python
updated 2.5 years ago by 45k • written 2.5 years ago by • 0
1
vote
3
replies
1.6k
views
take user options before calling snakemake
args snakemake sequencing python analysis
2.5 years ago by H.Hasani ★ 1.0k
3
votes
4
replies
2.8k
views
gff to gtf missing gene id
transcriptomics annotation
updated 2.5 years ago by 45k • written 2.5 years ago by • 0
0
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0
replies
632
views
bulk RNAseq matrix design and donor effect correction
RNA-SEQ limma combat batch-effect DESeq2
updated 2.5 years ago by 45k • written 2.5 years ago by • 0
2
votes
4
replies
1.4k
views
About the hegemony of BioPython
BioPython
updated 2.5 years ago by 22k • written 2.5 years ago by ▴ 10
1
vote
13
replies
3.2k
views
Can you swap reference genome releases ?
grch38 Reference-genome patch
2.5 years ago by jonas.andersson ▴ 40
4
votes
4
replies
1.6k
views
Question about a public scRNA dataset(single end)?
single-cell scRNA
updated 2.5 years ago by 45k • written 3.4 years ago by ▴ 60
0
votes
0
replies
813
views
Input file for Synteny visualization with SynVisio
Genomics Analysis Comparative Synteny
2.5 years ago by shwetamgr1 ▴ 20
0
votes
0
replies
613
views
Compare mice gene expressions to human gene expressions for IBD
NGS RNA-Seq
updated 2.5 years ago by 89k • written 2.5 years ago by • 0
0
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0
replies
1.2k
views
Job: International Summer School on Epigenetics & Genome Stability in Health, Ageing & Disease in Mainz, Germany
Research Internship Summer-School Summer-Internship
updated 2.5 years ago by 45k • written 2.5 years ago by ▴ 40
0
votes
0
replies
628
views
normalization and integration of two independent single cell cohorts
single-cell batch-effect normalization
updated 2.5 years ago by 45k • written 2.5 years ago by ▴ 260
0
votes
0
replies
467
views
Feature count no Result
RNA-Seq
2.5 years ago by Muhammad • 0
0
votes
0
replies
738
views
Understand the CellReads.stat file output from STARsolo
statistics star starsolo
updated 2.5 years ago by 45k • written 2.5 years ago by • 0
0
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0
replies
3.6k
views
Tool: euka: Robust detection of eukaryotic taxa from modern and ancient environmental DNA using pangenomic reference graphs.
pangenomics vg sedaDNA graph environmental-DNA
updated 2.5 years ago by 45k • written 2.5 years ago by ▴ 10
17
votes
7
replies
5.7k
views
None of the keys entered are valid keys for 'ENSEMBL'. Please use the keys method to see a listing of valid arguments.
Genemap
2.5 years ago by imran • 0
2
votes
4
replies
1.8k
views
bedtools intersect zero output
bedtools biomart
updated 2.3 years ago by 45k • written 2.5 years ago by ▴ 10
0
votes
0
replies
1.1k
views
ANNOVAR filter based annotation - ClinVar
Annovar clinvar
updated 2.5 years ago by 45k • written 2.5 years ago by ▴ 70
0
votes
0
replies
1.5k
views
Error trying to run FindMarkers using future (in parallel)
future scRNAseq FindMarkers Seurat parallel
updated 2.5 years ago by 154k • written 2.5 years ago by ▴ 20
0
votes
0
replies
631
views
Anyone familiar with ICGC's DCC data releases?
cancer TCGA PCAWG ICGC somatic
2.5 years ago by ConvolutedGenome ▴ 60
0
votes
0
replies
679
views
allelic copy number variation
LOH CNA CNV copy-number
updated 2.5 years ago by 45k • written 2.5 years ago by ★ 1.4k
2
votes
3
replies
1.6k
views
Any way to retrieve the annotation information of genomes under a bioproject ? (NCBI)
NCBI PGAP Bioproject annotation
2.5 years ago by v.berriosfarias ▴ 140
1
vote
1
reply
624
views
Distance Matrix
Matrix with Distance Beta Carbon
updated 2.5 years ago by 154k • written 2.5 years ago by • 0
0
votes
5
replies
1.2k
views
What do "local", "non-local", and "external" features mean regarding protein secondary structures?
protein assignment secondary-structure
2.5 years ago by 4fzcgueyp5 • 0
2
votes
4
replies
1.5k
views
NCBI protein id to gene id mapping for deleted entries
OrthoDB NCBI Entrez
2.5 years ago by niklas.endres • 0
2
votes
28
replies
3.9k
views
how do I generate frame 5 and 6 from the complementary strand?
python
updated 2.5 years ago by 45k • written 2.5 years ago by • 0
0
votes
1
reply
780
views
Tool: TRcaller : a novel Tool for SSR /STR/TR genotyping from NGS data for short and long reads
SSR NGS genotype STR
updated 2.5 years ago by 45k • written 2.5 years ago by • 0
5
votes
2
replies
4.0k
views
Issues while running java -jar gatk-package-4.4.0.0-local.jar
Gatk linux WES
updated 2.5 years ago by 89k • written 2.5 years ago by ▴ 10
0
votes
3
replies
1.4k
views
Heatmap from count matrix
heatmap R
updated 2.5 years ago by 89k • written 2.5 years ago by ▴ 30
0
votes
1
reply
1.6k
views
Q. BioPython: CodeML FileNotFoundError: [WinError 2]
paml biopython
updated 2.5 years ago by • 0 • written 6.7 years ago by • 0
0
votes
0
replies
399
views
Error when running BridgePRS
BridgePRS
2.5 years ago by Mengna Zhang ▴ 10
0
votes
0
replies
527
views
How can I get taxa relative abundances from HUMAnN?
metagenomics humann biobakery metatranscriptomics
2.5 years ago by O.rka ▴ 750
3
votes
6
replies
2.7k
views
bam index chromosome size limit
bam sam mapping rna-seq
updated 2.2 years ago by • 0 • written 2.5 years ago by • 0
2
votes
7
replies
1.8k
views
why CombineGCVFs in gatk not showing all the samples name?
haplotypecalling CombineGVCFs GATK
updated 2.5 years ago by 45k • written 2.5 years ago by ▴ 20
2
votes
4
replies
1.6k
views
PLINK Error: Invalid QUAL value on line
vcf plink plink2 qual
2.5 years ago by panacotaforcota • 0
2
votes
1
reply
1.6k
views
HTSeq count stranded setting
RNA-seq
updated 2.5 years ago by 103k • written 2.5 years ago by ▴ 30
3
votes
0
replies
1.2k
views
Herald: The Biostar Herald for Monday, April 10, 2023
herald
2.5 years ago by Biostar 3.6k
0
votes
0
replies
557
views
How to annotate PennCNV data using Annovar
PennCNV Annovar
2.5 years ago by Viktor Messi • 0
0
votes
0
replies
703
views
Producing ATAC count matrix for multiple samples
ATAC-Seq MACS2 Galaxy
2.5 years ago by jamescook365 • 0
1
vote
2
replies
1.3k
views
How to identify Gap location
Gap scaffold location
2.5 years ago by Takuma ▴ 20
0
votes
1
reply
680
views
Help in replicating LDSC heritability estimates
LDSC
2.5 years ago by Jerry ▴ 10
0
votes
1
reply
725
views
RSEM expression values
RSem Trinity
updated 2.5 years ago by 45k • written 2.5 years ago by • 0
0
votes
5
replies
1.3k
views
CNA plots with gene names using GISTIC
visualization CNA GISTIC
2.5 years ago by Bhaswatee • 0
0
votes
0
replies
560
views
ATAC: Finding peaks in BW file
ATAC bigwig
2.5 years ago by weimichelles • 0
0
votes
0
replies
527
views
Confused with macs has a same result when my input files are BED 3 and BED 5 format
peak-calling macs
updated 2.5 years ago by 45k • written 2.5 years ago by • 0
2
votes
3
replies
1.1k
views
Problem while executing bedtools sort
genome bedtools
updated 2.5 years ago by 45k • written 2.5 years ago by ▴ 140
1
vote
0
replies
738
views
News: Announcing the 3rd round of the Nextflow and nf-core mentorship
nf-core mentorship nf_core nextflow
updated 2.5 years ago by 45k • written 2.5 years ago by ▴ 610
0
votes
1
reply
948
views
problem with downloading htseq
htseq
updated 2.5 years ago by 154k • written 2.5 years ago by ▴ 10
0
votes
5
replies
1.3k
views
Going from pubmed esearch to protein fasta sequences: Biopython
protein fasta Biopython Entrez
2.5 years ago by m.brathwaite • 0
122,008 results • Page 273 of 2441
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C: What Does Cds And Exon Mean In A Gtf File?
A: What Does Cds And Exon Mean In A Gtf File?
Answer: Still confused about exons versus CDS
Publicly Available WGS Samples for Panel of Normals?
Comment: Recommendations for 200 SNP markers genotyping
Recommendations for 200 SNP markers genotyping
Answer: Recommendations for 200 SNP markers genotyping
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Recent Replies
Comment: DESeq2 on metagenome KO counts by ATpoint 89k
Both vst or logcpm will favor expression level (magnitude of counts) rather than differences in a hclust/heatmap. For differences you need …
Comment: DESeq2 on metagenome KO counts by ATpoint 89k
The DESeq2 developer has advised many times against DESeq2 for metagenomics. Please search for related posts over at support.bioconductor.o…
Answer: DESeq2 on metagenome KO counts by andres.firrincieli 3.9k
I wouldn’t use DESeq2 on aggregated raw counts per KO, because doing so means accepting two pretty big assumptions: 1. All genes with t…
Answer: DESeq2 on metagenome KO counts by Aleksandra ▴ 180
(I apologise for my previous reply; I wanted to be as detailed as possible) DESeq2 handles KO counts perfectly well. For a time-series des…
Comment: DESeq2 on metagenome KO counts by Aleksandra ▴ 180
I apologise for how that sounded; I wanted to be as detailed as possible.
Comment: GUI commercial software for 10x single cell gene expression analysis by Istvan Albert 103k
A comment on: "*Wonky analysis is possible even with open-source R libraries.*" True - and arguably, the risk of a wonky analysis is actua…
Comment: GUI commercial software for 10x single cell gene expression analysis by GenoMax 154k
`Trailmaker` likely only supports Parse's evercode data. <br> `BioTuring` does not appear to have published pricing. <br> `Rosalind` appear…
Answer: GUI commercial software for 10x single cell gene expression analysis by firestar ★ 1.7k
Found a few more when I asked around. I have no idea how good or bad these are. If anyone has used these or knows more about these, feel fr…
Comment: How to handle TrEMBL proteins without gene annotation in plasma proteomics? by GenoMax 154k
> I performed a standard proteomics screening workflow What database did you use to search against? Perhaps you are using an old (not so c…
Answer: FACS quality control based on size and doublet detection in scRNA-seq by ATpoint 89k
No, it's unrelated. Doublets in 10x happen if two cells get enclosed into the same GEM droplet. This has nothing to do with how flow cytome…
Answer: How to handle TrEMBL proteins without gene annotation in plasma proteomics? by Elisabeth Gasteiger ★ 2.4k
Apparently you are working with human proteins? I would strongly recommend looking only at proteins that are part of the human reference pr…
Comment: Tools to simulate Illumina short read sequences and ONT long reads with a refere by colindaven 8.0k
Wow, thats too long. How much RAM does your machine have, it is likely swapping
Comment: How to handle TrEMBL proteins without gene annotation in plasma proteomics? by Elisabeth Gasteiger ★ 2.4k
Note that UniProtKB accession numbers do not have any meaning. While most ACs starting with A0A5* are indeed unreviewed (i.e. from TrEMBL),…
Comment: DESeq2 on metagenome KO counts by young_bioinformatician ▴ 240
Thank you but sorry, your answer sounds very AI-based...
Answer: How to handle TrEMBL proteins without gene annotation in plasma proteomics? by Aleksandra ▴ 180
For basic analysis, discard anything that isn't from Swiss-Prot. Your statistics and pathway analysis should only be based on reliable, ann…
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