Limit : this week
all time today this week this month this year
170 results • Page 1 of 4
Sort: Views
Rank Views Votes Replies
40
votes
10
replies
42k
views
8 follow
Batch effects : ComBat or removebatcheffects (limma package) ?
limma sva Combat batch-effect
updated 1 day ago by ▴ 40 • written 6.7 years ago by ★ 1.3k
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
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 4 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
14
votes
2
replies
7.0k
views
Trouble with Pilon installation
polishing pilon installation
updated 6 days ago by • 0 • written 7.3 years ago by ★ 1.4k
7
votes
7
replies
5.9k
views
6 follow
How to know synonymous and non-synonymous SNPs from transcriptome sequencing
RNA-Seq SNP
updated 5 days ago by ▴ 850 • written 6.1 years ago by ▴ 10
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
2
votes
6
replies
3.7k
views
Treatment VS Control in Single Cell RNAseq analysis
Single Cell RNAseq DE Analysis Treatment Control
updated 5 days ago by 82k • written 3.9 years ago by ▴ 280
1
vote
6
replies
2.8k
views
Segmentation fault using gemma
gemma gwas
updated 2 days ago by • 0 • written 4.9 years ago by ▴ 90
0
votes
4
replies
2.7k
views
Lositan freezing when generating selection table
LOSITAN
updated 6 days ago by • 0 • written 8.3 years ago by • 0
2
votes
4
replies
2.6k
views
When to use .vcf or .gvcf files from GATK HaplotypeCaller?
indel gatk calling snp variant
updated 1 day ago by 9.7k • written 24 months ago by ▴ 120
0
votes
9
replies
2.5k
views
6 follow
Cannot process all the reads in a fast5 file?
metagenome base-calling fastq nanopore
updated 2 days ago by 43k • written 8 months ago by • 0
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
3
votes
3
replies
2.4k
views
How to make a TSS enrichment plot in ATAC-seq analysis?
ATAC
updated 5 days ago by • 0 • written 22 months ago by ▴ 180
4
votes
9
replies
2.1k
views
Legend and hap files for imputation with 38 build
reference 38build impute imputation
1 day ago by anna ▴ 20
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
37
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 3 days ago by ▴ 580
2
votes
7
replies
1.2k
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
1
vote
10
replies
962
views
Troubleshooting RNA-seq data with DNA contamination
RNA-seq DESeq2 DNA-contamination
6 days ago by DKA ▴ 40
2
votes
5
replies
919
views
Retrieval of Active site information programmatically
Catalytic Python Active PDB site Site
updated 1 day ago by ★ 2.0k • written 2.0 years ago by • 0
8
votes
16
replies
914
views
How to convert plink files to Hapmap Format
GWAS Plink
updated 4 days ago by ★ 2.4k • written 7 weeks ago by • 0
2
votes
11
replies
866
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
1
vote
8
replies
830
views
Adding CB tag to bam file
samtools bam
updated 6 days ago by 161k • written 12 days ago by • 0
0
votes
2
replies
819
views
AGeNT LocatIt
AGeNT LocatIt WES UMI duplicates
updated 6 days ago by ★ 2.1k • written 2.8 years ago by ▴ 10
0
votes
1
reply
739
views
Can I run cellassign on samples independently if there is batch effect present?
RNA-Seq R cellassign batch-effect
updated 3 days ago by ▴ 10 • written 3.3 years ago by ▴ 30
0
votes
3
replies
700
views
Why cd-hit-est not work when sequence identity threshold<0.95？
genome cluster sequence
updated 1 day ago by • 0 • written 21 months ago by • 0
4
votes
7
replies
663
views
7 follow
Heatmap and rna-seq
RNA-Seq Heatmap
updated 4 days ago by ★ 5.9k • written 8 days ago by ▴ 10
5
votes
16
replies
633
views
How many reads for WGS Sequencing?
WGS Bacterial-Genomics
2 days ago by Ruqaiya • 0
4
votes
8
replies
621
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
8
votes
8
replies
615
views
PCA plot (Suggestions Needed)
DESeq2 PCAplot
updated 6 days ago by 14k • written 7 days ago by ▴ 10
0
votes
0
replies
559
views
Correlation between cell type prediction scores and individual gene expression in spatial transcriptomic datasets
single-cell Spatial-Transcriptomics
4 days ago by biocellbio • 0
4
votes
7
replies
550
views
Very low RNA splicing rate for pulmonary AT2 cells
RNA-velocity scVelo scRNA-seq splicing
1 day ago by e.r.zakiev ▴ 200
0
votes
11
replies
545
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo scRNA-seq STAR snRNA-seq MGI
5 days ago by atowns21 • 0
0
votes
1
reply
485
views
GAPIT p-value significance threshold
GAPIT p-value GWAS
updated 5 days ago by • 0 • written 4 months ago by • 0
4
votes
7
replies
479
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
1
vote
7
replies
472
views
ScRNA data question
scRNA Vlnplot Samples
updated 1 day ago by ★ 2.4k • written 5 days ago by ▴ 10
0
votes
10
replies
471
views
Low mapping rate with Salmon
RNA-seq Salmon Quantification
updated 1 day ago by 19k • written 8 days ago by • 0
1
vote
7
replies
461
views
gvcf joint calling
WES GATK VCF gVCF
3 days ago by zihanss • 0
2
votes
5
replies
437
views
Fetch table from clinvar database according to a list of rsid
python clinvar perl
2 days ago by ashaneev07 ▴ 20
4
votes
4
replies
425
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
1
vote
8
replies
422
views
Downsampling fastq file
downsample fastq
20 hours ago by marco.barr ▴ 80
5
votes
6
replies
406
views
Programmatically retrieving positions of protein active site residues
Uniprot PDB Proteins
updated 21 hours ago by ▴ 760 • written 2 days ago by ▴ 40
4
votes
2
replies
388
views
Missing protein (VEGF-A) in String db
VGFA stringdb
updated 5 days ago by • 0 • written 11 weeks ago by ▴ 20
0
votes
8
replies
388
views
What does it mean single base resolution in sequencing?
SNP sequencing
updated 18 hours ago by 4.2k • written 2 days ago by ▴ 10
0
votes
5
replies
375
views
How should I make kallisto indexes?
kallisto
updated 1 day ago by ★ 5.9k • written 15 days ago by ▴ 150
1
vote
4
replies
367
views
Limma Analysis Agilent Microarray Data (GPL1708)
Microarray Limma Agilent
2 days ago by hagl ▴ 10
1
vote
3
replies
367
views
Help understanding how KEGG Ortholog `K00004 ` has 3 ECs associated with it (EC:1.1.1.4, 1.1.1.-, 1.1.1.303)?
ontology metagenomics database enzymes genomics
updated 2 days ago by ★ 27k • written 4 days ago by ▴ 710
0
votes
3
replies
366
views
why renaming Idents in Seurat object doesn't work?
Seurat RenameIdents R
22 hours ago by Assa Yeroslaviz ★ 1.8k
1
vote
3
replies
357
views
PCA plot
DESeq2 PCAplot
updated 2 days ago by 4.2k • written 6 days ago by ▴ 10
0
votes
5
replies
351
views
Is it possible to get a list of representative genomes from a past RefSeq release?
representative ncbi asembly refseq
updated 6 days ago by 141k • written 6 days ago by ▴ 90
170 results • Page 1 of 4
Recent Votes
Comment: Minimum RAM and Storage requirement for creating PSSM using ncbi-blast-2.2.30+-x
Answer: Discrepancy between Log2(x) and Log2(x+1) regarding Log2FC
Answer: Verify if all the components of a pathway are present in a genomes
Answer: p-value in CIBERSORT
Answer: Can I have multiple active GDC download tokens?
Answer: Can I have multiple active GDC download tokens?
Comment: Can I have multiple active GDC download tokens?
Recent Locations • All
United States, 2 minutes ago
Sheffield, UK, 7 minutes ago
United States, 8 minutes ago
Palau, 9 minutes ago
United States, 11 minutes ago
United States, 12 minutes ago
United States, 14 minutes ago
Recent Awards • All
Popular Question to elcortegano ▴ 200
Teacher to i.sudbery 19k
Popular Question to mathavanbioinfo ▴ 90
Popular Question to Jautis ▴ 530
Popular Question to Jonathan Yoou ▴ 60
Popular Question to Chris ▴ 260
Commentator to Lluís R. ★ 1.2k
Recent Replies
Comment: Post-imputation plot by kl ▴ 10
All of them are G/C and A/T variants Some seem mismatches based on AF and some seem to need flipping. I guess I am confused, as in the Mich…
Comment: Minimum RAM and Storage requirement for creating PSSM using ncbi-blast-2.2.30+-x by Nafi • 0
Thank you for the reply I have 16 gb of RAM then I can give a try then.
Comment: Alternatives to metanalyisis. P integration. Horiztonal integration RNA-seq by i.sudbery 19k
Can you give more details of the data you are planning to use. What is the different studies, what are the comparisons you want to make.
Comment: p-value in CIBERSORT by michelafrancesconi9 ▴ 20
Thank you so much!!
Comment: POSSUM not working due to incompatible pssm file by Ram 43k
Please use the formatting bar (especially the `code` option) to present your post better. You can use backticks for inline code (\`text\` b…
Comment: after selecting specific GO terms to plot, cneplot is not showing any color for by Ram 43k
Please use the formatting bar (especially the `code` option) to present your post better. You can use backticks for inline code (\`text\` b…
Comment: Telescope issue by GenoMax 141k
Looks like there is a tab missing between the sequence and the quality string.
Comment: Post-imputation plot by LChart 3.9k
I would pull out the variants with panel_freq ~ 1 - upload_freq and min(panel_freq, upload_freq) < 0.4. I would check if these are G/C or A…
Comment: Telescope issue by eleven11 • 0
Hello the output is A01940:33:GW2208142379th:3:1317:24126:3505 355 chr14 16651125 0 150M = 17034150 122900 GCTAACAGAGTTGAACCTTTCTATTG…
Comment: What does 'bundle_uuid' refer to in this metadata sheet? by GenoMax 141k
Looking at the [code here][1] `bundle_uuid` seems to be related to the submissions to HCA. Samples that ran on multiple lanes seem to have …
Comment: What does it mean single base resolution in sequencing? by LauferVA 4.2k
this is very true and increasingly true as time goes forward. thanks for supplementing this post with your own :-)
Comment: What does 'bundle_uuid' refer to in this metadata sheet? by jeffrey.maurer.informatics • 0
Thank you, but I've already checked out that site to see if I was missing anything and I don't see any answers to my questions there.
Answer: p-value in CIBERSORT by Aspire ▴ 320
You have not explicitly specified the number of permutations (which are used to calculate the p-value). The default value of the permutatio…
Comment: Telescope issue by GenoMax 141k
> CIGAR and query sequence are of different length [W::sam_read1] Parse error at line 9954941 Problem appears to be at that line. Can you …
Comment: KEGG Pathways by Ram 43k
Give us as much detail as you can. What error does it give you?
Traffic: 1891 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6