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158 results • Page 3 of 4
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0
votes
0
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67
views
absolute path for symbolic links in Snakefile
Snakemake
updated 7 hours ago by 43k • written 7 hours ago by ▴ 60
0
votes
0
replies
65
views
scRNA Cluster frequency
CV PCA scRNA Cluster-Frequency
7 hours ago by Nitin • 0
0
votes
0
replies
55
views
agilent microarray gpl data does not have gene symbol column
microarray agilent gpl
updated 5 hours ago by 43k • written 7 hours ago by • 0
0
votes
0
replies
55
views
Using samtools with GCS (google cloud storage) on docker a docker container seems to give "Protocol Not Supported" error
samtools gcs
4 hours ago by abhishekghadge • 0
0
votes
2
replies
136
views
how to find genes that are significantly expressed in brain cortex samples
rna-seq gene-expression
2 hours ago by rheab1230 ▴ 140
0
votes
0
replies
33
views
Removing Illumina microarray probes with no expression HumanHT-12v4
Low expression microarray HumanHT-12v4 Illumina
2 hours ago by Bioinformatician • 0
0
votes
0
replies
17
views
GTF file from Stringtie to R Studio for either Ballgown or DESeq2
Stringtie Cufflinks Ballgown DESeq2
36 minutes ago by Nina • 0
0
votes
3
replies
299
views
10x GEX and ADT data analysis in Seurat
Seurat scRNA-seq ADT Cite-seq GEX
updated 6 days ago by 81k • written 8 days ago by • 0
0
votes
0
replies
12
views
CpGtools no output
methylation cpgtools
30 minutes ago by Anna • 0
0
votes
0
replies
176
views
Core SNP tree VS. concatenated core genome tree
phylogenetic tree SNP
6 days ago by YiweiZhu ▴ 30
0
votes
2
replies
303
views
Help with understanding the identifier mapping tables in the backend of HUMAnN
metagenomics metacyc enzyme biobakery humann
6 days ago by O.rka ▴ 710
0
votes
0
replies
184
views
Somatic and Germline variant calling for tumor, normal and blood sample
germline variants somatic
updated 6 days ago by 43k • written 6 days ago by • 0
0
votes
0
replies
180
views
Novel cyclic peptide structure prediction
protein structure-prediction alphafold peptide
updated 5 days ago by 43k • written 5 days ago by • 0
0
votes
0
replies
155
views
Plotting heatmap of genes in each samples scRNA in Seurat
scRNA heatmap
5 days ago by Hien • 0
0
votes
0
replies
136
views
FreeBayes detection capacity
reads freebayes long
4 days ago by quentinperriere • 0
0
votes
0
replies
128
views
Repeat expansion identification tools for long-read data
fragilex repeatexpansion long-read fmr1
4 days ago by adarsh_pp ▴ 40
0
votes
0
replies
126
views
Automated internal stop codon checker
ORF stopcodon internal virus
4 days ago by Balazs Horvath ▴ 10
0
votes
4
replies
322
views
Compute bootstrap values on consensus tree
phylogeny tree raxml
4 days ago by pablo ▴ 300
0
votes
0
replies
136
views
How should I make kallisto indexes?
kallisto
updated 4 days ago by 141k • written 4 days ago by ▴ 150
0
votes
6
replies
518
views
PacBio adapters in transcriptome assembly from short read data?
adapter transcriptome sequencing pacbio vecscreen
4 days ago by Dunois ★ 2.5k
0
votes
1
reply
171
views
Two databases: Human Microbiome Project and MGnify
Microbiome databases
updated 4 days ago by 141k • written 4 days ago by ▴ 360
0
votes
0
replies
881
views
Advice on group specific condition effect and model matrix in deseq2
deseq2 batch-effect
updated 4 days ago by 43k • written 4.1 years ago by ▴ 330
0
votes
3
replies
1.1k
views
Batch effect for SNP array
sva combat batch-effect SNP
updated 4 days ago by 43k • written 4.2 years ago by ▴ 10
0
votes
2
replies
236
views
How to identify gaps in a genome?
awk seqkit assembly fasta genome
4 days ago by rj.rezwan • 0
0
votes
1
reply
190
views
merging Seurat objects after SCT
Seurat SCT
updated 4 days ago by 43k • written 4 days ago by • 0
0
votes
1
reply
172
views
How to get the reference panel sites for TOPMed hg37 and 38
Imputation
updated 4 days ago by ★ 2.3k • written 4 days ago by • 0
0
votes
0
replies
110
views
Add geno header to VariantAnnotation objects
nichenet scRNA-seq
3 days ago by QX • 0
0
votes
2
replies
241
views
RNAseq 1 control 2 different treatment
RNA-seq
3 days ago by matteo.levorato • 0
0
votes
0
replies
127
views
GWAS Phenotypes
GWAS
3 days ago by solomoncharles77 ▴ 90
0
votes
2
replies
230
views
Statistical Advice Needed for RNAseq Data Analysis
Statistical-Significance Genomics RNA-seq Data-Analysis
updated 3 days ago by 43k • written 4 days ago by • 0
0
votes
0
replies
133
views
what exactly is a k-mer table (remora)?
remora basecall
3 days ago by anne • 0
0
votes
0
replies
121
views
How to summarize dbCAN3 results
dbCAN CAZy CAZyme dbCAN3 dbCAN2
3 days ago by Nishat • 0
0
votes
2
replies
264
views
Merging Outputs from plink --assoc and --hardy to Produce Table
PLINK PANDAS R
3 days ago by Koketso • 0
0
votes
0
replies
130
views
Input into WGCNA and Error on constructNetworks on RNA-Seq data - unique rownames
rownames RNA-Seq WGCNA unique
3 days ago by shasabhi1 • 0
0
votes
5
replies
2.0k
views
Batch effect correction & normalization after training/test split for gene expression data
RNA-seq batch-effect normalization
updated 3 days ago by 43k • written 20 months ago by ▴ 60
0
votes
0
replies
1.3k
views
which value from ruvadj in missMethyl can present methylation status
R RUV methylation missmethyl batch-effect
updated 3 days ago by 43k • written 5.9 years ago by ▴ 20
0
votes
0
replies
1.5k
views
minifi for RRBS
rrbs batch-effect methylation
updated 3 days ago by 43k • written 7.1 years ago by ★ 2.9k
0
votes
0
replies
1.1k
views
Finding wobble/redundant positions in an RNA string using R.
RNA wobble-position R
updated 3 days ago by 43k • written 6.2 years ago by ▴ 100
0
votes
0
replies
835
views
Estimating sequence complexity of DNA sequence from fasta file
sequence RepeatMasker pacbio
updated 3 days ago by 43k • written 5.6 years ago by ▴ 10
0
votes
0
replies
1.4k
views
Help with Circos plot "Assumption Error" that prevents plotting a protein interactions network
CircosPlot
updated 3 days ago by 43k • written 3.3 years ago by • 0
0
votes
0
replies
1.1k
views
Extra adjustment variables during batch effect correction
rna-seq ComBat batch-effect
updated 3 days ago by 43k • written 4.3 years ago by ▴ 360
0
votes
9
replies
1.2k
views
Normalization across different single cell RNAseq experimetns
global-scaling single-cell scRNA-seq batch-effect
updated 2 days ago by 43k • written 3.9 years ago by ▴ 20
0
votes
0
replies
2.6k
views
Removing batch effects from methylation beta values for molecular subtyping/cluster analysis
clustering beta-values batch-effect methylation
updated 2 days ago by 43k • written 6.7 years ago by • 0
0
votes
1
reply
1.2k
views
Controlling for batch and estrus cycle using DESeq2 in RNA-seq analysis
random-effects RNA-Seq batch-effect
updated 2 days ago by 43k • written 6.7 years ago by • 0
0
votes
0
replies
1.7k
views
Accounting for hidden batch effects in differential expression analysis with DEXseq and Slueth
Batch-effect RNA-Seq Differential-Expression
updated 2 days ago by 43k • written 7.1 years ago by ▴ 270
0
votes
0
replies
2.8k
views
TCGA RNAseqVer2 batch effects
TCGA RNA-Seq batch-effect
updated 2 days ago by 43k • written 8.5 years ago by • 0
0
votes
7
replies
6.0k
views
Pre-processing of RNA-Seq data for WGCNA
RNA-Seq WGCNA removeBatchEffect DESeq2
updated 2 days ago by 43k • written 7.6 years ago by ▴ 70
0
votes
0
replies
1.8k
views
How to get Gene Co-expression Network from RNA seq data using cor() function?
RNA-Seq gene-expression-matrix correlation R
updated 2 days ago by 43k • written 6.3 years ago by ▴ 30
0
votes
0
replies
1.5k
views
RIPSeeker viewRIP function fails to extract values() in GRangesList/S4 object
RIPSeq S4 RIP R
updated 2 days ago by 43k • written 6.2 years ago by ▴ 80
0
votes
0
replies
2.7k
views
Comparing lists generated by Counter() and .most_common() for AA seqs
python amino-acid
updated 2 days ago by 43k • written 9.9 years ago by ★ 2.7k
158 results • Page 3 of 4
Recent Votes
bcftools multiple commands
bcftools pipe generated file from first command with second
C: How to setup a Summarized Experiment
A: How to download genome assemblies from NCBI with a list of GCA identifiers?
what's the genomic location and name of gene responsible for orange and black patches in calico cats
Comment: featureCounts --primary tag counting uniquely mapped reads and excludes multi-ma
Answer: Duplicate marking, read names, and the SRA
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Answer: MEGA Analysis Issue on High-Performance Computer by Mensur Dlakic ★ 27k
> I have ensured that I am using the latest version of MEGA and that other applications are not consuming excessive resources during the an…
Comment: Installing/switching between versions of R/Rstudio/Bioconductor on personal mach by BioinfGuru ★ 1.7k
Some of us are still learning and fall foul to knowledge limitation fairly regularly. Luckily we have people to put us in our place.
Answer: Running blastp with BLAST+ 2.15.0 against custom database; need to identify hits by GenoMax 141k
> I know that I should be able to collect protein sequences from the blastp results into a file, but I do not know how to do this. You c…
Comment: how to find genes that are significantly expressed in brain cortex samples by rheab1230 ▴ 140
I got the normalized gene count from gtex portal. they use inverse quantile normalization
Comment: what's the genomic location and name of gene responsible for orange and black pa by Matthias Zepper 4.5k
It is not entirely off, but evidently also not correct. Melanin biosynthesis is a multistep process, that indeed prominently involves the…
Comment: Installing/switching between versions of R/Rstudio/Bioconductor on personal mach by Ram 43k
> so a single Rscript could utilise multiple environments and versions How is that sane, let alone "better"? Also, why use `snap` for curl…
Comment: how to find genes that are significantly expressed in brain cortex samples by Ram 43k
Normalized how?
Comment: Duplicate marking, read names, and the SRA by GenoMax 141k
With public data one has to work with what is there. If the information about position is absent then only thing that could be done is to l…
Comment: Installing/switching between versions of R/Rstudio/Bioconductor on personal mach by BioinfGuru ★ 1.7k
Or better yet. To have an R package that allows access to conda environments via "conda list env" so that environments can be switched with…
Comment: what's the genomic location and name of gene responsible for orange and black pa by GenoMax 141k
If GPT is right then it says that: > The specific gene responsible for the orange and non-orange (black or > gray) fur colors in cats is t…
Comment: what's the genomic location and name of gene responsible for orange and black pa by Jean-Karim Heriche 27k
As far as I know the Orange locus hasn't been mapped to a gene. Maybe this paper will help in narrowing the search: https://www.ncbi.nlm.ni…
Comment: Duplicate marking, read names, and the SRA by Luka • 0
>Curios if there a reference for this? [Apparently it's not deprecated yet][1], but will be soon and the SRA intends for it to be at some …
Comment: Installing/switching between versions of R/Rstudio/Bioconductor on personal mach by Ram 43k
I prefer RStudio for new projects as well. The moment I need versions though, RStudio becomes a burden. I wish one could launch RStudio fro…
Comment: what's the genomic location and name of gene responsible for orange and black pa by GenoMax 141k
According to ChatGPT: The gene responsible for the orange and black patches of fur in calico cats (and tortoiseshell cats) is the X-linked …
Comment: Installing/switching between versions of R/Rstudio/Bioconductor on personal mach by BioinfGuru ★ 1.7k
Certainly true. Switching versions is way simpler that way, at the cost of the familiarity of the Rstudio IDE - especially if the code is w…
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