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How to show relabel sub cluster on the original cluster in Seurat
scRNA-seq seurat cluster clustering
updated 4.0 years ago by ★ 1.1k • written 4.0 years ago by • 0
13
votes
7
replies
9.1k
views
6 follow
Extract Sub_Tree From Big Phylogeny
phylogeny
updated 4.0 years ago by ▴ 10 • written 12.8 years ago by ▴ 760
0
votes
1
reply
1.8k
views
R error @rpath/libicuuc.54.dylib
script R
updated 4.0 years ago by 12k • written 4.0 years ago by • 0
1
vote
0
replies
676
views
Phylogenetic Tree
Ancestral Phylogenetic MSA Sequence Tree
4.0 years ago by satyam85cool ▴ 10
0
votes
2
replies
2.4k
views
converting annovar format file to maf by annovarToMaf
maftools annovarToMaf ANNOVAR MAF
4.0 years ago by Zahra ▴ 110
0
votes
0
replies
750
views
Cutadapt de-multiplexing does not recognize some barcodes
demultiplexing Deep-sequencing cutadapt
4.0 years ago by Rezenman • 0
0
votes
1
reply
1.1k
views
How can I know the BLAST percentage from kraken2 files ?
kraken2 BLAST
updated 4.0 years ago by 35k • written 4.0 years ago by ▴ 10
3
votes
3
replies
1.6k
views
Create genome-unique intervals from overlapping records in a bed file
bedtools ranges BED genomic
4.0 years ago by c0tton • 0
1
vote
4
replies
1.4k
views
Differential expression analysis between two different cohorts
RNA-Seq TCGA R
4.0 years ago by leticia ▴ 20
3
votes
6
replies
1.9k
views
Differential gene abundance analysis with 16s seq data
gsea 16s GO bacteria
4.0 years ago by ic23oluk • 0
0
votes
9
replies
3.0k
views
Microarray analysis in R - target.txt,file,Sample info
R
updated 2.5 years ago by 45k • written 4.0 years ago by ▴ 60
0
votes
4
replies
1.9k
views
ABOUT affymetrix genotyping console (GTC) software and TCGA CNV workflow
affymetrix TCGA CNV GTC
4.0 years ago by xingyu ▴ 10
1
vote
3
replies
3.8k
views
What is the Sleuth intercept and how can Sleuth be used when you have >2 treatment types?
RNA-Seq sleuth kallisto salmon DTE
updated 6.8 years ago by ▴ 10 • written 8.7 years ago by ▴ 100
0
votes
0
replies
805
views
Wild type breast primary cell miRNA data
Breast cancer miRNA control Cancer
4.0 years ago by jaqx008 ▴ 110
2
votes
2
replies
1.3k
views
Workshop for population genomics
Genomics
updated 2.6 years ago by 45k • written 4.0 years ago by • 0
0
votes
0
replies
667
views
Integrative analysis scRNAseq
scrnaseq
4.0 years ago by SG ▴ 20
1
vote
0
replies
669
views
Chip seq remove the genes which has very low enrichment
Deeptools ChIP-Seq Sequencing R
4.0 years ago by Lalita ▴ 10
0
votes
0
replies
762
views
How to use Picrust to make functional profile has as input a the taxonomic abundance table from MG-rast ?
MG-rast 16S PICRUST Metagenome and
4.0 years ago by Wydemberg • 0
0
votes
3
replies
1.4k
views
ROC_AUC curve for performance of a classification
curve ROC AUC
updated 4.0 years ago by 89k • written 4.0 years ago by ▴ 10
0
votes
1
reply
834
views
Problem loading my multifasta
Multifasta
updated 4.0 years ago by 153k • written 4.0 years ago by • 0
2
votes
12
replies
4.6k
views
6 follow
PROVEAN not working
provean
updated 3.2 years ago by • 0 • written 5.3 years ago by ▴ 20
1
vote
5
replies
2.0k
views
Python doesn't switch between different each environments in Anaconda.
Anaconda Python
updated 4.0 years ago by 89k • written 4.0 years ago by ▴ 80
5
votes
2
replies
1.3k
views
Most well regarded piRNA detection pipeline/program
expression piRNA differential smallRNAseq detection
4.0 years ago by RNAseqer ▴ 280
3
votes
4
replies
3.2k
views
Which files from PacBio output files to use in downstream analysis in R
R PacBio
updated 2.5 years ago by 45k • written 4.0 years ago by ▴ 20
7
votes
3
replies
3.0k
views
Forum: Misuse of RPKM or TPM normalization when comparing across samples and sequencing protocols
fpkm paper tpm
updated 4.0 years ago by 89k • written 4.0 years ago by ▴ 20
1
vote
1
reply
1.7k
views
Difference in .bed target region base count and mapped base count for different tools
samtools software gatk
updated 2.3 years ago by 45k • written 5.6 years ago by • 0
2
votes
3
replies
2.1k
views
Using HTSeq-count for paired-end data but unsorted by SAMTOOLS
htseq ngs
4.0 years ago by ChocoParrot ▴ 20
0
votes
2
replies
1.1k
views
Tools or Method for batch analysis of Paired end WES data in a queue way.
Pipeline Queue Batch Exome Data-Analysis
updated 3.2 years ago by 45k • written 4.0 years ago by ▴ 20
1
vote
6
replies
2.0k
views
gff file
GFF UNIPRTOT
updated 2.5 years ago by 45k • written 4.0 years ago by ▴ 10
2
votes
2
replies
2.3k
views
bad file format in HMM file
hmmpress hmmer
4.0 years ago by pavelasquezv ▴ 50
0
votes
0
replies
734
views
FRPK and RSEM
RNA-seq NGS FPKM
updated 3.3 years ago by 45k • written 4.0 years ago by ▴ 10
5
votes
1
reply
1.5k
views
News: New biostar-tools metaport for FreeBSD
freebsd software
4.0 years ago by bacon4000 ▴ 80
0
votes
0
replies
1.0k
views
extract IDs from each population in PLINK .fam file and export to .txt separately
plink fam bash
4.0 years ago by pabe ▴ 30
11
votes
10
replies
5.2k
views
edgeR design matrix error not of full rank
edgeR contrastmatrix design glmfit
updated 4.0 years ago by ★ 8.3k • written 4.0 years ago by • 0
0
votes
5
replies
1.5k
views
how can I run the catastrophy program?
linux catastrophy
4.0 years ago by pavelasquezv ▴ 50
0
votes
0
replies
678
views
Jaccard Distance
Jaccard genotyping
4.0 years ago by QAZ ▴ 20
1
vote
4
replies
3.0k
views
Per sequence GC content still not good after trimming
GC content. trimmomatic.
updated 4.0 years ago by 153k • written 4.0 years ago by • 0
1
vote
1
reply
1.1k
views
Dealing with missing values in population allele frequency data in classifier model bulding context
allele ML frequency missing_value classifier
4.0 years ago by Hamid Ghaedi 3.3k
0
votes
0
replies
848
views
Automating busted in Hyphy
Hyphy phylogenetics. BUSTED
updated 4.0 years ago by 153k • written 4.0 years ago by • 0
2
votes
2
replies
2.0k
views
How to find differences between single cell RNA seq samples beyond cluster information and differential expression?
rna-seq single-cell
updated 4.0 years ago by 45k • written 4.0 years ago by ▴ 10
0
votes
0
replies
795
views
Doubt about adonis( ) on Beta diversity matrix
Adonis
4.0 years ago by leandro • 0
0
votes
1
reply
1.2k
views
Problem with minfi package
minfi methylation analysis package DNA
updated 3.9 years ago by ▴ 10 • written 4.0 years ago by • 0
2
votes
4
replies
6.4k
views
Generating volcano plots of high and low expressed gene in scRNAseq data?
cell RNAseq scRNAseq single
updated 3.9 years ago by 89k • written 4.0 years ago by • 0
1
vote
2
replies
1.8k
views
Ways to Speed Up Mafft?
mafft hpc
4.0 years ago by andrew • 0
0
votes
1
reply
883
views
TCGA single dataset normalization
DESeq2 normalization
updated 4.0 years ago by 89k • written 4.0 years ago by • 0
1
vote
1
reply
1.0k
views
Haplogrep classify error
haplogroup mitochondria haplogrep
updated 2.0 years ago by • 0 • written 4.0 years ago by ▴ 10
1
vote
2
replies
2.4k
views
Complex Heatmap/InteractiveComplexHeatmap Error fontawesome 5.13.0
ComplexHeatmap fontawesome InteractiveComplexHeatmap
updated 4.0 years ago by ▴ 220 • written 4.0 years ago by • 0
1
vote
1
reply
1.0k
views
Difference between dataset analysis
Dataset analysis
updated 4.0 years ago by 89k • written 4.0 years ago by ▴ 30
1
vote
9
replies
3.7k
views
The BLAST command stops with an error.
RNA-seq BLAST Trinity blastx
updated 4.0 years ago by 15k • written 4.0 years ago by ▴ 80
0
votes
1
reply
1.4k
views
How to best predict effect for each variant and count specific effect found in each individual using variant effect predictor?
vcf vep
updated 4.0 years ago by 24k • written 4.0 years ago by ▴ 140
121,896 results • Page 569 of 2438
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Answer: Is a direct comparison of the number of up- and down-regulated genes meaningful?
allele frequency in VCF
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Answer: TCGA -derived Large RangeSummarizeExperient file
Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
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Recent Replies
Comment: Pipeline for downloading, aligning, and curating influenza A and B sequences for by GenoMax 153k
Have you looked at https://nextstrain.org/ and specifically https://github.com/nextstrain/seasonal-flu Software is available to do the ana…
Comment: Different UMAP for batch correction in R and Pytho by GenoMax 153k
Use this tutorial for how to upload images: https://www.biostars.org/p/309884/#346553 Only difference is instead of using an external imag…
Answer: GTEx sQTL v8 – annotation version used? by GenoMax 153k
If you click over to the `Reference` tab ( https://gtexportal.org/home/downloads/adult-gtex/reference ), it looks like they used GENCODE v.…
Comment: How to Identify Conserved 21-mers Across TE Insertions in Drosophila? by manikin_python9f ▴ 20
Since they are transposons, we don’t know the exact location of them. We know their sequence of insertions from repeatmasker in dm6 genome.…
Comment: Tool 'sra_source' does not exist. by Atefeh • 0
Thanks for your kindness.
Comment: TCGA -derived Large RangeSummarizeExperient file by Tom • 0
It works well. Thank you very much ! @atpoint
Answer: TCGA -derived Large RangeSummarizeExperient file by ATpoint 89k
For the end user these `DFrames` are just regular data.frames, so you can do `col_data[,c("barcode", "patient", "whatever")]` or just do `a…
Comment: magpurify errors by shevch2009 ▴ 20
I have checked with my eyes, and I didn't find it, I have only one contig that starts with k127_458 .... but the name is different - k127_4…
Comment: Yeast reference-based genome assembly by Michael 56k
So, you aren't sure about the exact species? Then you might want to be careful with reference-based assembly in general. I recommend the fo…
Comment: Structural Variant identification on pangenome graphs by Panos ★ 1.8k
That's a very comprehensive list! Thanks for sharing! `minigraph` better suits my needs because all I need is SVs for my genomes. As far a…
Comment: Yeast reference-based genome assembly by amy967107 • 0
I have ~2.01 Gb of ONT data and the target genome is ~20–23 Mb (90–100× coverage). My ONT read N50 is ~3.8 kb, so contiguity may be limited…
Comment: Yeast reference-based genome assembly by amy967107 • 0
This is a yeast strain (probably Rhodotorula spp.) and I'm trying to assemble the entire genome from nanopore reads using a reference-based…
Answer: Yeast reference-based genome assembly by Michael 56k
The new [hifiassm ONT][1] may be all you need for getting a good assembly. I would not recommend LRSDAY, except for its annotation part (wh…
Comment: magpurify errors by Mensur Dlakic ★ 30k
By the way, these errors are not unique. If you look through the `magpurify` GitHub issues, both types have been reported already. - https…
Comment: magpurify errors by Mensur Dlakic ★ 30k
There is absolutely no chance that a contig labeled `k127_4584534` doesn't exist in your fasta files. These names are not made up out of th…
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