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1,000 results • Page 1 of 20
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98
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106
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46k
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26 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
1000genomes PLINK PCA
updated 19 days ago by ▴ 20 • written 5.7 years ago by 87k
76
votes
72
replies
19k
views
19 follow
Tutorial: Clustering of DAVID gene enrichment results from gene expression studies
enrichment david
3 days ago by Kevin Blighe 87k
103
votes
42
replies
31k
views
34 follow
Forum: List of cloud genomics companies
cloud-genomics
updated 19 days ago by 22k • written 10.5 years ago by ★ 3.6k
10
votes
37
replies
12k
views
21 follow
Convert Gene IDs of Tomato Sol Database
tomato gene
updated 18 days ago by • 0 • written 8.8 years ago by ▴ 170
10
votes
36
replies
5.8k
views
Design in DESeq: Can you combine explicit and implicit batch effect correction in (SVA+Metadata Variables)?
SVA batch-effect DESeq2 R
updated 11 days ago by 43k • written 5.7 years ago by ▴ 620
81
votes
27
replies
20k
views
12 follow
ATAC-seq sample normalization
ChIP-Seq atac-seq normalization
updated 25 days ago by • 0 • written 4.4 years ago by ▴ 240
87
votes
24
replies
23k
views
17 follow
Tutorial: Gene Set Enrichment Analysis
microarray enrichment RNA-Seq GSEA
updated 10 days ago by • 0 • written 3.5 years ago by 3.2k
23
votes
23
replies
9.9k
views
6 follow
How to see if adjusting batch effect in RNA-seq is working or not
RNA-Seq removeBatchEffect batch-effect edger
updated 10 days ago by 43k • written 5.3 years ago by ▴ 130
11
votes
22
replies
4.2k
views
No significant DEG: A request to double check my commands for limma.
limma differential-gene-expression
updated 18 days ago by 43k • written 5.0 years ago by ▴ 260
13
votes
22
replies
11k
views
SVA : Setting up the data from an ExpressionSet and applying sva function to extimate batches
sva combat batch-effect
updated 11 days ago by 43k • written 6.8 years ago by ★ 1.3k
57
votes
22
replies
28k
views
7 follow
Batch correction in DESeq2
Combat DESeq2 Batch-Effect
updated 22 days ago by 43k • written 4.5 years ago by ▴ 510
5
votes
20
replies
4.2k
views
Differential gene expression from RNAseq data. Before or after annotation?
differential-gene-expression RNA-seq
updated 18 days ago by 43k • written 6.2 years ago by ▴ 90
18
votes
20
replies
4.4k
views
6 follow
How to identify significant differentially expressed genes and gene regulatory networks from microarray data.
microarray differential-gene-expression
updated 18 days ago by 43k • written 7.5 years ago by ▴ 80
7
votes
20
replies
6.4k
views
7 follow
Repeat masked gtf files from ensembl
ensembl RNA-Seq genome
updated 17 days ago by ▴ 200 • written 4.3 years ago by ▴ 80
22
votes
18
replies
6.1k
views
about batch correction in scRNA-seq
scRNA scRNA-seq batch-effect
updated 9 days ago by 43k • written 4.6 years ago by ★ 1.4k
2
votes
18
replies
1.6k
views
error when running phg create-maf-vcf to build a built practical haplotype graph (v2)
pangenome phg_v2 plants PHG
26 days ago by b.contreras.moreira ▴ 170
6
votes
17
replies
6.6k
views
Can you add a label key to heatscatter plot in R?
heatscatter visualization R
updated 11 days ago by 43k • written 9.6 years ago by ▴ 100
12
votes
17
replies
6.1k
views
9 follow
ACMG assignment tools
wes acmg WES WGS
updated 24 days ago by • 0 • written 3.9 years ago by ▴ 180
8
votes
16
replies
863
views
How to convert plink files to Hapmap Format
GWAS Plink
updated 1 day ago by ★ 2.4k • written 7 weeks ago by • 0
34
votes
16
replies
20k
views
9 follow
Filtration Of Reads With Length Lower Than 30 From Bam
read length bam
updated 9 days ago by ▴ 10 • written 10.2 years ago by ▴ 180
3
votes
16
replies
2.7k
views
design matrix for dge
limma differential-gene-expression r
updated 18 days ago by 43k • written 7.9 years ago by ▴ 50
17
votes
16
replies
14k
views
10 follow
How to extract the longest isoform from multi fasta file
perl extract fasta python isoform
updated 25 days ago by • 0 • written 9.8 years ago by ▴ 310
0
votes
16
replies
1.1k
views
What is the sequence origin in human plasma?
human sequence cfDNA
15 days ago by biwdpang • 0
22
votes
14
replies
28k
views
7 follow
removing batch effects using ComBat and SVA
SVA ComBat R Batch-effect
updated 19 days ago by 43k • written 7.9 years ago by ▴ 280
5
votes
14
replies
990
views
Not getting any modification calls in nanopore reads with dorado basecaller
mofications dorado basecalling nanopore methylation
updated 17 days ago by 141k • written 5 weeks ago by ▴ 20
5
votes
13
replies
1.2k
views
Tutorial: Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
R Ubuntu Linux Bioconductor Rstudio
updated 8 days ago by 82k • written 9 days ago by ★ 1.7k
5
votes
13
replies
9.2k
views
8 follow
biomaRt: Timeout on getBM().
r biomart ensembl
updated 17 days ago by ★ 2.0k • written 2.8 years ago by ▴ 40
12
votes
13
replies
4.4k
views
RNA-Seq DGE using PCA components as covariate
differential-gene-expression RNA-Seq glm DESeq2
updated 18 days ago by 43k • written 6.2 years ago by ★ 1.6k
13
votes
13
replies
18k
views
9 follow
How Do I Translate Multiple (More Than 25000) Dna Sequences With Different Frames To Protein Seuquence?
dna protein
updated 20 days ago by • 0 • written 10.3 years ago by ▴ 170
0
votes
13
replies
3.5k
views
6 follow
Tax4Fun2 - error
tax4fun silva blast
updated 4 days ago by • 0 • written 2.2 years ago by ▴ 10
4
votes
13
replies
876
views
RNAseq of primary tumor and metastases in two different organ
metastases RNA-seq DEG R
updated 11 days ago by ★ 1.7k • written 17 days ago by • 0
8
votes
12
replies
1.9k
views
Metric to use for RNAseq expression matrix
gene-expression TPM RNA-Seq counts batch-effect
10 days ago by Ram 43k
9
votes
12
replies
4.1k
views
Batch effect, how to create a model matrix
RNA-Seq deseq2 batch-effect
updated 10 days ago by 43k • written 4.9 years ago by ▴ 330
11
votes
12
replies
975
views
Downloaded pdb's on rcsb.org
rcsb pdb
updated 9 days ago by 43k • written 9 days ago by • 0
30
votes
12
replies
3.8k
views
Trying to understand the maths behind one Limma function
limma RNA-Seq batch-effect
updated 12 days ago by 43k • written 4.0 years ago by ▴ 330
54
votes
12
replies
28k
views
12 follow
Out Of Disk Space With Picard Tools ?
picard
updated 9 days ago by • 0 • written 12.0 years ago by ★ 2.9k
3
votes
12
replies
547
views
struggle to get fasta files from ucsc goldenPath
ucsc getfasta fasta
26 days ago by Lila M ★ 1.2k
5
votes
12
replies
1.6k
views
Subbmission Data
RNA-seq
updated 25 days ago by 43k • written 14 months ago by ▴ 50
8
votes
12
replies
3.5k
views
Why should ATAC-seq mapped reads be shifted +4 and -5 for +strand and -strand, respectively
ATAC-seq
updated 25 days ago by • 0 • written 3.4 years ago by ▴ 40
4
votes
11
replies
649
views
Redirection of Duplicate PMIDs
pubmed pmid
updated 4 days ago by 4.2k • written 5 days ago by • 0
0
votes
11
replies
513
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo scRNA-seq STAR snRNA-seq MGI
2 days ago by atowns21 • 0
1
vote
11
replies
573
views
Removing adapter/primer sequence from reads while keeping flanking regions
trimming fasta cutadapt BBDuk fastq
23 days ago by Bryan ▴ 10
11
votes
11
replies
1.2k
views
7 follow
How I know if it is a batch effect or are real differences between my controls and treatments?
RNA-seq Transcriptomics ComBat-seq Batch-Effect
updated 19 days ago by 141k • written 21 days ago by ▴ 10
25
votes
11
replies
3.7k
views
6 follow
Forum: Site Use Guidelines
meta biostars Guidelines
updated 4 days ago by 43k • written 14.6 years ago by 100k
6
votes
11
replies
3.3k
views
Collapsing probesets to genes on WGCNA
WGCNA gene-expression R
updated 11 days ago by 43k • written 5.2 years ago by ▴ 120
3
votes
11
replies
6.0k
views
Modifying R pairs() function
plotMEpairs WGCNA R
updated 11 days ago by 43k • written 6.4 years ago by ▴ 30
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 1 day ago by ★ 3.8k • written 10.8 years ago by ▴ 920
23
votes
11
replies
4.9k
views
7 follow
Code golf: detecting homopolymers of length N in the (human) genome
code golf fasta homopolymer repeat
updated 11 days ago by 43k • written 5.0 years ago by 47k
8
votes
10
replies
717
views
bash script
whole-genome-sequencing
updated 12 days ago by 43k • written 20 days ago by ▴ 30
9
votes
10
replies
4.4k
views
Using rnaseq reference sample across batches
RNA-Seq batch-effect
updated 11 days ago by 43k • written 7.4 years ago by ▴ 30
1,000 results • Page 1 of 20
Recent Votes
Comment: How to assign cell types after integration in scRNA
NGS forensics: how to know if data is fabricated
Answer: ChIP-seq datasets: input samples omitted?
Comment: Help understanding how KEGG Ortholog `K00004 ` has 3 ECs associated with it (EC:
A: Deeptools plotHeatmap - Maintain Order of Input BED file
Comment: NGS forensics: how to know if data is fabricated
Comment: calculate nucleotide diversity from whole-genome-sequence data for individual ge
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Recent Replies
Comment: How many reads for WGS Sequencing? by Ruqaiya • 0
Also, there is no mention of adapter sequence so which adapter sequence should i use to remove it from some other reads?
Comment: How many reads for WGS Sequencing? by Ruqaiya • 0
Also, Do you think i can reproduce at least most part of the data from the paper just on my laptop? It has 4 logical processors (Intel(R) C…
Comment: NGS forensics: how to know if data is fabricated by Philipp Bayer 8.3k
While I think this is an interesting case, I've before found cleaned 'raw' data on SRA. It happens: bioinformaticians receive the raw data,…
Comment: How many reads for WGS Sequencing? by Ruqaiya • 0
1. What does clipped Fastq mean? both forward and reverse reads in the same file? 2. Why would you remove 2000bp contigs? I feel it will gi…
Comment: How many reads for WGS Sequencing? by Ruqaiya • 0
Well, I downloaded both the reads from-[LINK][1]. Thats all i did. Thats the only thing i need to do, right? I'l try spades. [1]: http…
Comment: How to assign cell types after integration in scRNA by Francesco ▴ 10
Thanks for the fast reply.. however i had only partially understood the answer. Is correct saying that low-representation integration and b…
Answer: Can I run cellassign on samples independently if there is batch effect present? by Francesco ▴ 10
Hi! Whenever you do make independent analysis or aggregate data and analyze them, most cell type assignment tools start from raw counts to …
Comment: gvcf joint calling by zihanss • 0
Thanks for your comment, I get it now.
Answer: ChIP-seq datasets: input samples omitted? by ATpoint 82k
In my hands (and from what I know based on many years here) inputs are almost exclusively used during peak calling to correct for loci-spec…
Comment: How to assign cell types after integration in scRNA by ATpoint 82k
No difference here. After all you typically want a label per cluster/group, so either subset to the control condition to do the assignment,…
Comment: Differential Expression using Isoseq-supplemented reference transcriptome by gaoanwei • 0
I found the question and ASK the GPT4 turbo
Answer: Differential Expression using Isoseq-supplemented reference transcriptome by gaoanwei • 0
Your approach seems reasonable and well-informed, though it's perhaps less customary in the field, which could be why you haven't found pap…
Answer: How many reads for WGS Sequencing? by Mensur Dlakic ★ 27k
It takes 29 seconds to assemble this genome (20 CPUs) with the following statistics: 135 contigs, total 2821177 bp, min 200 bp, max …
Comment: NGS forensics: how to know if data is fabricated by noodle ▴ 530
IMO (and unfortunately) there needs to be an effort to develop these algorithms.
Comment: gvcf joint calling by Jeremy Leipzig 22k
the samples that are `./.` have no coverage (or not enough to call a genotype) and the `0/0` are homozygous reference
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