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1,000 results • Page 4 of 20
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4
votes
7
replies
813
views
Help with weighted nearest neighbor analysis
seurat single-cell
8 months ago by Chris ▴ 280
4
votes
11
replies
686
views
Remove X in row name with only number
GSVA
updated 3 months ago by 43k • written 3 months ago by ▴ 280
4
votes
5
replies
399
views
Filter out miRNA from ncRNA dataset
bowtie bowtie2 miRNA filtering ncRNA
updated 10 weeks ago by 82k • written 11 weeks ago by ▴ 10
4
votes
7
replies
2.4k
views
Batch effects vs biological variables
Batch-effect DESeq2 combat_seq
updated 29 days ago by 43k • written 3.7 years ago by ▴ 20
4
votes
6
replies
1.1k
views
Python script to automatically read in, name output files & parse R1 & R2 fastq.gz files when given an input directory with raw data files
python fastq
9 months ago by eorr ▴ 30
4
votes
5
replies
2.4k
views
Merge CNVnator output of multiple samples
CNV WGS
updated 10 months ago by 43k • written 6.7 years ago by ▴ 40
4
votes
3
replies
713
views
How to interpret output of PLINK association test (--assoc)
assoc
updated 8 months ago by 11k • written 8 months ago by ▴ 10
4
votes
4
replies
3.3k
views
Unable to install Autogrid4
autogrid software-error autogrid4
updated 11 months ago by 43k • written 3.2 years ago by • 0
4
votes
4
replies
660
views
Feedback on mouse brain scRNA-seq quality control
mouse brain singe-cell scRNAseq quality-control
8 months ago by nshenoy ▴ 50
4
votes
5
replies
544
views
Which refseq_protein db to choose for zingiberaceae
local blastp blast
updated 9 months ago by 142k • written 9 months ago by • 0
4
votes
9
replies
2.7k
views
Blast+ remote database names
blast remote databases Blastplus
updated 9 months ago by 142k • written 2.3 years ago by • 0
4
votes
6
replies
1.2k
views
Transcript quantification
rna-seq transcriptome SRA
updated 10 months ago by 82k • written 10 months ago by • 0
4
votes
3
replies
770
views
Creating custom GTF file for use with Cellranger with barcode sequences
Cellranger
8 months ago by stefano.iantorno ▴ 70
4
votes
6
replies
1.1k
views
Pre-processing for single cell RNAseq: Hard thresholds, data (cluster)-driven or both?
scRNA-seq
updated 7 months ago by ▴ 120 • written 7 months ago by ▴ 130
4
votes
11
replies
1.7k
views
Check Strandedness
Check_Strandedness how_are_we_stranded_here leafcutter bash
updated 6 months ago by 20k • written 8 months ago by • 0
4
votes
5
replies
1.1k
views
VEP run with --af_gnomadg refuses to provide allele frequencies for extremely rare variants
vep gnomad
updated 8 months ago by ▴ 60 • written 9 months ago by 22k
4
votes
9
replies
2.1k
views
Legend and hap files for imputation with 38 build
reference 38build impute imputation
8 days ago by anna ▴ 20
4
votes
3
replies
745
views
Why is there a big difference between the outputs of `geneBody_coverage` of `RSeQC` when using different bed files?
RSeQC
12 months ago by Dan ▴ 180
4
votes
4
replies
377
views
Average expression of a sample in single-cell data
single-cell rna-seq
5 weeks ago by newuser2024 • 0
4
votes
6
replies
960
views
Open-Source software. Good or bad for the market?
genomic-analysis software
updated 11 months ago by 43k • written 6.2 years ago by • 0
4
votes
7
replies
1.5k
views
.bed files from sequencing platform not containing intervals of "alt", "random" haplotypes. How do I perform coverage and haplotype caller?
exome .bed haplotypes HG38 coverage
updated 9 months ago by 142k • written 9 months ago by • 0
4
votes
3
replies
403
views
Single cell analysis of Cancer
cancer single-cell RNA-seq
updated 12 weeks ago by 142k • written 12 weeks ago by ▴ 20
4
votes
3
replies
610
views
Over Representation analysis altered pathways in common between comparisons plot
R Visualization DGE ORA
updated 7 months ago by ★ 2.0k • written 7 months ago by ▴ 10
4
votes
6
replies
856
views
bwa mem hangs after a few thousand reads
bwa alignment variant-calling bwa-mem
updated 5 weeks ago by 43k • written 5 months ago by ▴ 30
4
votes
6
replies
3.8k
views
How to interpret DEXseq results in therms of significance
DEXseq RNA-Seq exon
updated 1 day ago by ▴ 30 • written 6.7 years ago by ★ 1.2k
3
votes
4
replies
5.2k
views
What does this Warning in HTSeq-count means? (Warning: Mate pairing was ambiguous)
RNA-Seq
updated 9 months ago by ▴ 10 • written 8.7 years ago by ★ 1.4k
3
votes
4
replies
1.5k
views
fastPHASE -F provided to estimate haplotype frequencies, but no freqs in output
genomics phasing fastPHASE
updated 11 months ago by 43k • written 6.1 years ago by ▴ 10
3
votes
3
replies
512
views
Need Control Gene Count Files
R RNA-Seq TCGA
updated 6 months ago by ▴ 20 • written 6 months ago by ▴ 30
3
votes
5
replies
1.4k
views
AlphaMissense Plugin VEP
Plugin VEP Alphamissense
updated 7 months ago by 43k • written 7 months ago by ▴ 10
3
votes
3
replies
2.8k
views
WGCNA Labeled Heatmap
heatmap wgcna
updated 7 months ago by 43k • written 2.6 years ago by ▴ 40
3
votes
5
replies
277
views
Generating mpileup file using samtools
mpileup samtools
updated 4 days ago by 21k • written 4 days ago by • 0
3
votes
4
replies
4.1k
views
What are the Pros and Cons of working in Bioinformatics???
career bio
updated 11 months ago by 43k • written 6.2 years ago by ▴ 20
3
votes
4
replies
3.5k
views
any recommended tools for batch effect and normalization not written in R?
R RNA-Seq combat python batch-effect
updated 19 days ago by 43k • written 7.1 years ago by ▴ 310
3
votes
4
replies
792
views
Downstream analysis with DEseq2 normalization
DEseq2 integration
5 months ago by QX • 0
3
votes
3
replies
531
views
Free/open source 23andme-like analysis
SNPs genomics NGS VCF
updated 17 days ago by 14k • written 18 days ago by ▴ 580
3
votes
12
replies
976
views
why 99% reads failed to align in mir-seq analysis?
Fastqc bowtie1 miRNA-seq alignment differential-expression-analysis
3 months ago by mohammadhassanj ▴ 260
3
votes
5
replies
1.5k
views
Trouble with best practices
samtools WES NGS GATK
updated 11 months ago by 43k • written 6.2 years ago by • 0
3
votes
4
replies
658
views
Weighted analysis
RNA-seq
7 months ago by Peter • 0
3
votes
7
replies
506
views
Snakemake rule that runs an assessment for once after completing other previous rules
snakemake
8 weeks ago by Fadlilah ▴ 10
3
votes
3
replies
810
views
When counting ASVs in DADA2, does a hit/count only occur at 100% alignment percent identity?
metagenomics qiime2 amplicon 16s dada2
updated 8 months ago by 3.6k • written 9 months ago by ▴ 710
3
votes
6
replies
4.1k
views
how do Differential gene expression analysis by Salmon output
differential-gene-expression Salmon
updated 28 days ago by 43k • written 5.6 years ago by ▴ 100
3
votes
1
reply
554
views
chromosome location to gene name and aa change
variant-annotation
11 months ago by Zi • 0
3
votes
9
replies
803
views
Understanding this analysis pipeline
reads
updated 10 months ago by 43k • written 10 months ago by • 0
3
votes
8
replies
2.0k
views
Kallisto mapping paired end
Kallisto mapping
updated 12 months ago by 43k • written 2.2 years ago by ▴ 20
3
votes
3
replies
343
views
learning bioinformatics
course learning
updated 3 months ago by 43k • written 3 months ago by • 0
3
votes
2
replies
865
views
STAR aligner FATAL ERROR not correct
fastq star
updated 11 months ago by 43k • written 2.3 years ago by ▴ 10
3
votes
6
replies
855
views
scRNA-seq: Consistent low number of cells and low fraction reads across the samples
scRNA-seq cells mRNA expression gene
updated 5 months ago by ★ 1.8k • written 5 months ago by ▴ 40
3
votes
3
replies
346
views
Volcano Plot Output Inquiry: Graphs Facing Down
rstudio volcano-plot
5 weeks ago by Pumla • 0
3
votes
2
replies
1.2k
views
DESeq2 design and Batch effects
RNA-Seq batch-effect DESeq2
updated 20 days ago by 43k • written 4.4 years ago by ▴ 10
3
votes
7
replies
2.6k
views
6 follow
Online BLAST search using R
BLAST R
updated 11 weeks ago by ▴ 140 • written 2.8 years ago by ▴ 20
1,000 results • Page 4 of 20
Recent Votes
Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA
Answer: TFs and Gene databases
Answer: TFs and Gene databases
Answer: TFs and Gene databases
Answer: Understanding STAR output (Aligned.out.sam file)
Comment: High Malat-1 expression in single cell data
Comment: removeBatchEffect explained using base R linear models
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Recent Replies
Answer: Understanding STAR output (Aligned.out.sam file) by heelpPlease • 0
After thoroughly reviewing all the documents again, I've identified the root cause of my initial issue: the failure to detect essential gen…
Comment: Understanding STAR output (Aligned.out.sam file) by heelpPlease • 0
Thank you! Now that I understand that there is a difference between read and fragment, I could actually find a lot of helpful information..…
Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA by sovrappensiero ▴ 90
Thanks again. Hmm...this makes me suspicious of whether this normalization is actually possible. In case you'd like to take a look, [here]…
Comment: Filtering Multi-sample VCF file for all except one Genotype by Jeremy Leipzig 22k
The seven genotypes being 58025AA, 58025AG, 58051TT, 58051TC, 58051CC, 58057TT, 58057TC
Answer: TFs and Gene databases by jared.andrews07 ★ 16k
See [TFlink](https://tflink.net/), [KnockTF2](https://bio.liclab.net/KnockTFv2/index.php), [TFBSDB](https://tfbsdb.systemsbiology.net/), an…
Comment: Filtering Multi-sample VCF file for all except one Genotype by GenoMax 142k
> Seven genotpyes have been sampled and all variants, which belong to one of those genotpyes are to be "erased" (or every other variant exc…
Comment: Filtering Multi-sample VCF file for all except one Genotype by Pierre Lindenbaum 161k
> , filter a multisample VCF file for all genotypes except one of them filter for what ?
Answer: Applying the metacell2 algorithm using python by Wayne ★ 2.0k
I had hoped things like [this Jupyter notebook for the rabbit data analysis](https://nbviewer.org/github/tanaylab/rabembflow/blob/master/2-…
Comment: Help with running egsea() by 1769mkc ★ 1.2k
please provide the design matrix mean the metadata of the model fit2 which is there in the code . i guess other users can help
Comment: Applying the metacell2 algorithm using python by JACKY ▴ 140
The repo does not provide any valuable information unfortunately. The Metacell algorithm they provide in the vignette is missing the metagr…
Comment: Repeated testing/data mining in RNA Seq by robert.flynn.21 • 0
Thanks! I'll give it a go.
Comment: Applying the metacell2 algorithm using python by Wayne ★ 2.0k
Yes, they are very clear about this. The page about the Vignettes says: >"They are not meant as a comprehensive documentation of all the fe…
Comment: Gene density plot by dthorbur ★ 1.9k
This sounds like it would be a simple task in either python or R. Read data in, potentially with a library like `data.table` in `R`, depend…
Answer: HLA-HD tool for genomic imputation by Javier • 0
Hi, I just solved the same error. In my case, it was because I misunderstood the instructions. hlahd.sh -t 4 *-f ~/hlahd.1.7.0/fr…
Comment: Question regarding WGCNA by andres.firrincieli 3.6k
Ok, then. You likely have a scale free topology that look like this: [link][1] In this situation you should pick the power value with an …
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