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1,116 results • Page 1 of 23
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103
votes
42
replies
31k
views
34 follow
Forum: List of cloud genomics companies
cloud-genomics
updated 22 days ago by 22k • written 10.5 years ago by ★ 3.6k
99
votes
106
replies
46k
views
26 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
1000genomes PLINK PCA
updated 22 days ago by ▴ 20 • written 5.7 years ago by 87k
87
votes
24
replies
23k
views
17 follow
Tutorial: Gene Set Enrichment Analysis
microarray enrichment RNA-Seq GSEA
updated 12 days ago by • 0 • written 3.5 years ago by 3.2k
81
votes
27
replies
20k
views
12 follow
ATAC-seq sample normalization
ChIP-Seq atac-seq normalization
updated 27 days ago by • 0 • written 4.4 years ago by ▴ 240
76
votes
72
replies
19k
views
19 follow
Tutorial: Clustering of DAVID gene enrichment results from gene expression studies
enrichment david
5 days ago by Kevin Blighe 87k
57
votes
22
replies
29k
views
7 follow
Batch correction in DESeq2
Combat DESeq2 Batch-Effect
updated 25 days ago by 43k • written 4.5 years ago by ▴ 510
54
votes
12
replies
28k
views
12 follow
Out Of Disk Space With Picard Tools ?
picard
updated 12 days ago by • 0 • written 12.1 years ago by ★ 2.9k
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
37
votes
5
replies
13k
views
How do you generate TMM normalized counts using EdgeR?
R RNA-seq edgeR
updated 20 days ago by ▴ 60 • written 2.9 years ago by ★ 1.0k
37
votes
24
replies
1.7k
views
10 follow
NGS forensics: how to know if data is fabricated
fastq STAR NGS Illumina
updated 14 hours ago by 19k • written 3 days ago by ▴ 580
34
votes
16
replies
20k
views
9 follow
Filtration Of Reads With Length Lower Than 30 From Bam
read length bam
updated 11 days ago by ▴ 10 • written 10.2 years ago by ▴ 180
30
votes
12
replies
3.8k
views
Trying to understand the maths behind one Limma function
limma RNA-Seq batch-effect
updated 15 days ago by 43k • written 4.0 years ago by ▴ 330
25
votes
11
replies
3.7k
views
6 follow
Forum: Site Use Guidelines
meta biostars Guidelines
updated 7 days ago by 43k • written 14.6 years ago by 100k
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 13 days ago by 43k • written 5.3 years ago by ▴ 130
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 14 days ago by 43k • written 5.0 years ago by 47k
22
votes
18
replies
6.1k
views
about batch correction in scRNA-seq
scRNA scRNA-seq batch-effect
updated 12 days ago by 43k • written 4.6 years ago by ★ 1.4k
22
votes
14
replies
28k
views
7 follow
removing batch effects using ComBat and SVA
SVA ComBat R Batch-effect
updated 22 days ago by 43k • written 7.9 years ago by ▴ 280
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
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 21 days ago by 43k • written 7.5 years ago by ▴ 80
17
votes
8
replies
13k
views
9 follow
MAF vs VAF
sequencing
updated 27 days ago by ▴ 80 • written 6.1 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 27 days ago by • 0 • written 9.8 years ago by ▴ 310
15
votes
6
replies
1.3k
views
6 follow
VCF to human friendly form?
vcf visualization
updated 15 days ago by 161k • written 19 months ago by ▴ 10
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
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 13 days ago by 43k • written 6.8 years ago by ★ 1.3k
13
votes
10
replies
6.4k
views
Adjusting for confounding variables in RNA-SEQ Differential Expression Analysis
Differential-Gene-Expression RNA-Seq Statistics
updated 21 days ago by 43k • written 5.7 years ago by ▴ 40
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 22 days ago by • 0 • written 10.3 years ago by ▴ 170
12
votes
2
replies
459
views
News: 8th Berlin Summer School in NGS Data Analysis (June 10-14, 2024) - already half booked
Workshop RNA-Seq DNA-Seq Illumina
20 days ago by David Langenberger 11k
12
votes
13
replies
4.4k
views
RNA-Seq DGE using PCA components as covariate
differential-gene-expression RNA-Seq glm DESeq2
updated 21 days ago by 43k • written 6.2 years ago by ★ 1.6k
12
votes
4
replies
2.3k
views
long read + salmon? (transcript abundance)
long-read salmon
updated 25 days ago by 43k • written 14 months ago by ▴ 50
12
votes
17
replies
6.1k
views
9 follow
ACMG assignment tools
wes acmg WES WGS
updated 26 days ago by • 0 • written 3.9 years ago by ▴ 180
11
votes
9
replies
11k
views
10 follow
Genome assembly statistical tools
Assembly statistics
updated 17 days ago by • 0 • written 4.7 years ago by ▴ 10
11
votes
9
replies
7.0k
views
How to choose method to integrate different patient sample together in Seurat
Seurat scRNA batch-effect harmony
updated 13 days ago by 43k • written 4.2 years ago by ▴ 80
11
votes
12
replies
989
views
Downloaded pdb's on rcsb.org
rcsb pdb
updated 12 days ago by 43k • written 12 days ago by • 0
11
votes
6
replies
543
views
Pangenome of plant
pangenome plant
22 days ago by analyst ▴ 30
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 21 days ago by 141k • written 24 days ago by ▴ 10
11
votes
22
replies
4.2k
views
No significant DEG: A request to double check my commands for limma.
limma differential-gene-expression
updated 21 days ago by 43k • written 5.0 years ago by ▴ 260
10
votes
6
replies
9.9k
views
6 follow
CDS vs cDNA vs transcript for mapping RNA-Seq reads
Assembly rna-seq alignment
updated 4 days ago by ★ 5.1k • written 6.0 years ago by ▴ 510
10
votes
6
replies
14k
views
7 follow
How To Identify The 16S Rrna Gene Sequence In A Genome
updated 12 days ago by 6.4k • written 10.9 years ago by ▴ 10
10
votes
5
replies
1.4k
views
6 follow
Courses in RNAseq data
RNA-seq Courses
updated 28 days ago by 43k • written 2.6 years ago by ▴ 30
10
votes
7
replies
7.1k
views
6 follow
Convert GVF to VCF
vcf
updated 14 days ago by • 0 • written 9.3 years ago by ▴ 970
10
votes
37
replies
12k
views
21 follow
Convert Gene IDs of Tomato Sol Database
tomato gene
updated 20 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 13 days ago by 43k • written 5.7 years ago by ▴ 620
9
votes
4
replies
288
views
Ubuntu storage space is decreasing automatically
ubuntu storage
updated 21 days ago by 6.4k • written 21 days ago by ▴ 30
9
votes
5
replies
2.3k
views
Millions of Reads Needed for Differential Gene Expression
differential-gene-expression RNA-Seq deseq2
updated 21 days ago by 43k • written 4.6 years ago by ▴ 20
9
votes
4
replies
1.9k
views
Integration of RNA-Seq data with microarray data
microarray RNA-Seq batch-effect R
updated 13 days ago by 43k • written 4.0 years ago by ▴ 30
9
votes
10
replies
6.9k
views
Harmony batch correction vs. regressing out donor effect in Seurat
Seurat scRNA-seq Harmony RNA-seq batch-effect
updated 12 days ago by 43k • written 4.6 years ago by ▴ 140
9
votes
12
replies
4.1k
views
Batch effect, how to create a model matrix
RNA-Seq deseq2 batch-effect
updated 13 days ago by 43k • written 4.9 years ago by ▴ 330
9
votes
6
replies
1.5k
views
What in silico PCR commandline tool do you use that can handle IUPAC characters?
pcr amplicon primer
updated 28 days ago by 43k • written 16 months ago by ▴ 710
9
votes
3
replies
7.0k
views
EdgeR-GLMs correcting for batch effects
RNA-Seq edgeR Batch-Effect
updated 12 days ago by 43k • written 9.9 years ago by ▴ 250
9
votes
10
replies
4.4k
views
Using rnaseq reference sample across batches
RNA-Seq batch-effect
updated 13 days ago by 43k • written 7.4 years ago by ▴ 30
1,116 results • Page 1 of 23
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Answer: Verify if all the components of a pathway are present in a genomes
Answer: p-value in CIBERSORT
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Answer: Can I have multiple active GDC download tokens?
Comment: Can I have multiple active GDC download tokens?
Comment: Programmatically retrieving positions of protein active site residues
Comment: Programmatically retrieving positions of protein active site residues
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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?
Comment: What does 'bundle_uuid' refer to in this metadata sheet? by GenoMax 141k
SRA Run Selector shows a better view of the metadata: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA761679&o=acc_s%3Aa
Comment: Adjust pvalue in R with different approach give me all different outcome by Aspire ▴ 320
- `p.adjust()` is supposed to receive a **numeric vector of p-values**, not a matrix. - It makes no sense to "adjust" just one p-value, …
Comment: Downsampling fastq file by marco.barr ▴ 80
I understood where the problem lies. I discussed with my wet lab colleagues (this is part of a bioinformatician's job...) and by showing th…
Comment: Programmatically retrieving positions of protein active site residues by me ▴ 760
This question fits in nicely with the [SIB Swiss Institute of Bioinformatics course on Enzyme information in UniProt][1] [1]: https://w…
Answer: Programmatically retrieving positions of protein active site residues by me ▴ 760
This can be done via SPARQL at the UniProt.org sparql endpoint PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX fald…
Comment: KEGG Pathways by Sudip • 0
No it does not. Do you know of a way that can help me achieve what I want?
Comment: Minimum RAM and Storage requirement for creating PSSM using ncbi-blast-2.2.30+-x by GenoMax 141k
UniRef file is 43G compressed so probably will become ~60G when uncompressed. You would likely be looking at at least that much +10-20% GB …
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