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76
votes
72
replies
19k
views
19 follow
Tutorial: Clustering of DAVID gene enrichment results from gene expression studies
enrichment david
6 days ago by Kevin Blighe 87k
40
votes
10
replies
42k
views
8 follow
Batch effects : ComBat or removebatcheffects (limma package) ?
limma sva Combat batch-effect
updated 2 days ago by ▴ 40 • written 6.7 years ago by ★ 1.3k
38
votes
24
replies
1.8k
views
10 follow
NGS forensics: how to know if data is fabricated
fastq STAR NGS Illumina
updated 1 day ago by 19k • written 4 days ago by ▴ 580
19
votes
11
replies
14k
views
10 follow
How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
utr
updated 5 days ago by ★ 3.8k • written 10.8 years ago by ▴ 920
10
votes
6
replies
9.9k
views
6 follow
CDS vs cDNA vs transcript for mapping RNA-Seq reads
Assembly rna-seq alignment
updated 5 days ago by ★ 5.1k • written 6.0 years ago by ▴ 510
8
votes
8
replies
615
views
PCA plot (Suggestions Needed)
DESeq2 PCAplot
updated 6 days ago by 14k • written 7 days ago by ▴ 10
8
votes
16
replies
916
views
How to convert plink files to Hapmap Format
GWAS Plink
updated 5 days ago by ★ 2.4k • written 8 weeks ago by • 0
7
votes
7
replies
5.9k
views
6 follow
How to know synonymous and non-synonymous SNPs from transcriptome sequencing
RNA-Seq SNP
updated 6 days ago by ▴ 850 • written 6.1 years ago by ▴ 10
5
votes
16
replies
647
views
How many reads for WGS Sequencing?
WGS Bacterial-Genomics
2 days ago by Ruqaiya • 0
5
votes
3
replies
225
views
6 follow
Integrate transcriptomic data and proteomics data.
OMICS
updated 1 day ago by ★ 1.2k • written 1 day ago by • 0
5
votes
6
replies
433
views
Programmatically retrieving positions of protein active site residues
Uniprot PDB Proteins
updated 1 day ago by ▴ 760 • written 2 days ago by ▴ 40
4
votes
7
replies
556
views
Very low RNA splicing rate for pulmonary AT2 cells
RNA-velocity scVelo scRNA-seq splicing
2 days ago by e.r.zakiev ▴ 200
4
votes
0
replies
119
views
Herald: The Biostar Herald for Monday, April 29, 2024
herald
2 days ago by Biostar 2.7k
4
votes
2
replies
283
views
How to use limma to find differentially expressed genes in response to a continuous variable
limma voom R
2 days ago by pairedttest ▴ 10
4
votes
7
replies
482
views
To get p-values for the TPM
P-value TPM RSEM
updated 6 days ago by ★ 5.9k • written 7 days ago by • 0
4
votes
5
replies
265
views
High Malat-1 expression in single cell data
cell analysis single
updated 2 days ago by ★ 5.9k • written 2 days ago by ▴ 10
4
votes
2
replies
389
views
Missing protein (VEGF-A) in String db
VGFA stringdb
updated 5 days ago by • 0 • written 11 weeks ago by ▴ 20
4
votes
9
replies
2.1k
views
Legend and hap files for imputation with 38 build
reference 38build impute imputation
2 days ago by anna ▴ 20
4
votes
8
replies
625
views
Create a new bed file with all pairwise combinations between two other bed files, based on bp distance
SNPs BED eqtl bedtools
updated 4 days ago by 35k • written 5 days ago by ▴ 10
4
votes
4
replies
429
views
Tutorial: how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix RNAseq R
updated 4 days ago by ★ 1.7k • written 6 days ago by ★ 3.9k
4
votes
6
replies
3.8k
views
Taking the difference of two VCFs (or removing singletons)
genome sequencing singleton SNP filter
updated 1 day ago by ▴ 20 • written 9.6 years ago by ▴ 40
4
votes
3
replies
343
views
Source other conda environments in a nextflow pipeline when nextflow itself is in a conda environment?
hpc conda nextflow
updated 4 days ago by 3.2k • written 5 days ago by ▴ 40
4
votes
7
replies
667
views
7 follow
Heatmap and rna-seq
RNA-Seq Heatmap
updated 4 days ago by ★ 5.9k • written 8 days ago by ▴ 10
3
votes
3
replies
292
views
Is it possible to bulk download files from GEO repository?
RNA-seq Galaxy Tanscriptomics
updated 2 days ago by ▴ 580 • written 2 days ago by ▴ 750
3
votes
2
replies
343
views
Extract protein sequence
fasta alignment blast
1 day ago by anna ▴ 20
3
votes
3
replies
2.4k
views
How to make a TSS enrichment plot in ATAC-seq analysis?
ATAC
updated 6 days ago by • 0 • written 22 months ago by ▴ 180
3
votes
6
replies
2.0k
views
7 follow
DNA methylation preprocessing
SWAN DNA methylation Funnorm
updated 4 days ago by 43k • written 2.4 years ago by ▴ 10
3
votes
3
replies
295
views
Sequence read length shorter than flow cell specification
illumina NGS sequencing
updated 6 days ago by 14k • written 6 days ago by • 0
3
votes
2
replies
281
views
ChIP-seq datasets: input samples omitted?
ChIP-seq Normalization NGS
updated 2 days ago by 19k • written 5 days ago by ▴ 40
3
votes
0
replies
196
views
News: Webinar “Learning Single-cell Atlases” with Dr. Fabian Theis, author of Scanpy on May 8
Scanpy Generative-AI scRNA Machine-Learning
updated 5 days ago by 43k • written 5 days ago by ▴ 60
3
votes
4
replies
341
views
Why gatk VariantAnnotator required bam and coverage files
gatk VariantAnnotator
6 days ago by QX • 0
3
votes
3
replies
290
views
genome assembly records not present in assembly_summary.txt
ncbi bacteria assembly
updated 5 days ago by 141k • written 5 days ago by ▴ 10
3
votes
2
replies
324
views
what is the purpose of indexing the reference genome (Kallisto)
indexing Kallisto
updated 5 days ago by ★ 5.9k • written 5 days ago by ▴ 10
3
votes
7
replies
294
views
FastQC Quality per tile and per sequence behaving strange after using Cutadapt
fastqc cutadapt illumina tile paired-end
2 days ago by salias • 0
2
votes
4
replies
2.6k
views
When to use .vcf or .gvcf files from GATK HaplotypeCaller?
indel gatk calling snp variant
updated 2 days ago by 9.7k • written 24 months ago by ▴ 120
2
votes
6
replies
3.7k
views
Treatment VS Control in Single Cell RNAseq analysis
Single Cell RNAseq DE Analysis Treatment Control
updated 6 days ago by 82k • written 3.9 years ago by ▴ 280
2
votes
4
replies
268
views
from row count to tpm
tpm row-count normalization
updated 1 day ago by 43k • written 9 days ago by ▴ 20
2
votes
2
replies
205
views
p-value in CIBERSORT
CIBERSORT p-value
13 hours ago by michelafrancesconi9 ▴ 20
2
votes
1
reply
233
views
Finding orthologs between genome error
OMA OMAbrowser
updated 6 days ago by ★ 1.1k • written 7 days ago by • 0
2
votes
7
replies
1.3k
views
6 follow
Differential Expression using Isoseq-supplemented reference transcriptome
RNA-Seq Salmon Isoseq
updated 2 days ago by ★ 7.1k • written 8 months ago by ▴ 10
2
votes
11
replies
875
views
Questions about a bug when transferring cram file to bam file
sequence samtools bcftools
updated 2 days ago by ★ 1.2k • written 14 days ago by • 0
2
votes
5
replies
438
views
Fetch table from clinvar database according to a list of rsid
python clinvar perl
3 days ago by ashaneev07 ▴ 20
2
votes
2
replies
160
views
MA plot of shrunken fold change
MA-plot Deseq2
updated 1 day ago by 82k • written 1 day ago by • 0
2
votes
2
replies
187
views
PDB related issue
rcsb pdb
updated 2 days ago by ▴ 580 • written 3 days ago by • 0
2
votes
3
replies
346
views
How to establish haplotype-specific gene expression levels
RNA-seq Haplotype
updated 5 days ago by ★ 5.9k • written 22 days ago by ▴ 60
2
votes
5
replies
340
views
Figures are disappeared from html report of SnpEff
HTML SnpEff
2 days ago by analyst ▴ 30
2
votes
5
replies
329
views
How to trim transcripts using information from NCBI contamination screen report
RNAseq assembly transcriptome contamination
5 days ago by Lada ▴ 30
2
votes
4
replies
2.4k
views
How could I generate a gi_taxid_nucl.dmp file similar to the one previously hosted by NCBI?
ncbi metagenomics centrifuge gi_taxid_nucl.dmp taxonomy
updated 6 days ago by • 0 • written 2.4 years ago by • 0
2
votes
5
replies
919
views
Retrieval of Active site information programmatically
Catalytic Python Active PDB site Site
updated 2 days ago by ★ 2.0k • written 2.0 years ago by • 0
1
vote
0
replies
198
views
Job: CTO/founding engineer role at Voyant Bio
engineer
6 days ago by Assaf ▴ 10
166 results • Page 1 of 4
Recent Votes
C: TOPGO- how to do GO enrichment using a custom go database?
Answer: NGS forensics: how to know if data is fabricated
Comment: Adjust pvalue in R with different approach give me all different outcome
Comment: Bacterial plasmid analysis
Comment: DESeq2 processing problems
Comment: What does 'bundle_uuid' refer to in this metadata sheet?
What Is The Difference Between Structural Variants (Svs) And Copy-Number Variants (Cnvs)?
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Recent Replies
Comment: Post-imputation plot by kl ▴ 10
Ok yes I think my thought was that given these errors, I could remove the mismatches and flip the alleles which seem to need flipping based…
Comment: Bacterial plasmid analysis by nicole.kavanagh • 0
I think I will perhaps use their predominant PlasmidFinder type to group plasmids together and create separate core phylogenies for each as…
Comment: Bacterial plasmid analysis by GenoMax 141k
Can you classify the plasmids based on function (resistance genes they are carrying or some other criteria). Sizes above are indicating a w…
Comment: DESeq2 processing problems by ATpoint 82k
Initially posted here https://support.bioconductor.org/p/9158036/ where I suggested to put code and data and noted that GEOquery returns ar…
Answer: Post-imputation plot by LChart 3.9k
I agree that some need to be flipped (A/T and C/G where your panel frequency is 1 - ref panel frequency). There are other variants which yo…
Comment: RNA editing sites based on DNA seq and RNA seq by Adam ▴ 30
Are those 20% unaligned reads coming after hyper-editing detection?
Answer: How to find overlap of clusters in two seurat porject by Adam ▴ 30
I think your best bet would be to use annotation mapping. You can use the features of your clusters in group 1 and apply them to group 2 to…
Answer: DESeq2 processing problems by Adam ▴ 30
> when I put in the dataset, I am not able to run it for DEG analysis because system asks me to remove the first column which is of gene na…
Comment: Bacterial plasmid analysis by nicole.kavanagh • 0
Thank you so much for your quick response, I have been searching scientific papers for about a week but have failed to come up with a reaso…
Comment: Bacterial plasmid analysis by GenoMax 141k
> however I'm not sure this would be appropriate in my case as the plasmid sequences are obviously much more diverse and vary in size Can…
Answer: cnetplot category names are too long by bkleiboeker ▴ 370
I'm sure someone could find a more elegant solution using `stringr::str_wrap`, but for a one-time solution I did this: # my results of…
Comment: Telescope issue by GenoMax 141k
You could edit the SAM file but I wonder if this problem is present in your original fastq data file so if not inconvenient do the alignmen…
Comment: Mutect2 for mitochondria variant discovery by GenoMax 141k
> I keep getting error. Without providing information about the actual error no one can help. Please edit the post and add this informati…
Comment: Telescope issue by eleven11 • 0
Thank you! how would I correct that?
Comment: DESeq2 processing problems by Ram 43k
This is an open science community, not a place to write an email to Michael Love. Please address the entire community.
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