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1,000 results • Page
1 of 20
Sort: Votes
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Views
Votes
Replies
164
votes
70
replies
60k
views
34 follow
How To Efficiently Parse A Huge Fastq File?
fastq
next-gen-sequencing
updated 29 days ago by
Ram
43k • written 12.8 years ago by
Panos
★ 1.8k
103
votes
42
replies
31k
views
34 follow
Forum:
List of cloud genomics companies
cloud-genomics
updated 18 days ago by
Jeremy Leipzig
22k • written 10.5 years ago by
14134125465346445
★ 3.6k
98
votes
106
replies
46k
views
26 follow
Tutorial:
Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
1000genomes
PLINK
PCA
updated 18 days ago by
psb7
▴ 20 • written 5.7 years ago by
Kevin Blighe
87k
87
votes
24
replies
23k
views
17 follow
Tutorial:
Gene Set Enrichment Analysis
microarray
enrichment
RNA-Seq
GSEA
updated 8 days ago by
Gordon
• 0 • written 3.5 years ago by
Hamid Ghaedi
3.2k
81
votes
27
replies
20k
views
12 follow
ATAC-seq sample normalization
ChIP-Seq
atac-seq
normalization
updated 23 days ago by
sgv
• 0 • written 4.3 years ago by
Flo
▴ 240
76
votes
72
replies
19k
views
19 follow
Tutorial:
Clustering of DAVID gene enrichment results from gene expression studies
enrichment
david
1 day ago by
Kevin Blighe
87k
57
votes
22
replies
28k
views
7 follow
Batch correction in DESeq2
Combat
DESeq2
Batch-Effect
updated 21 days ago by
Ram
43k • written 4.5 years ago by
Arindam Ghosh
▴ 510
54
votes
12
replies
28k
views
12 follow
Out Of Disk Space With Picard Tools ?
picard
updated 8 days ago by
kjngo
• 0 • written 12.0 years ago by
Gabriel R.
★ 2.9k
49
votes
30
replies
11k
views
13 follow
Tutorial:
How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
documentation
meta
how-to
updated 29 days ago by
Istvan Albert
100k • written 8.2 years ago by
Ram
43k
39
votes
9
replies
42k
views
6 follow
Batch effects : ComBat or removebatcheffects (limma package) ?
limma
sva
Combat
batch-effect
updated 9 days ago by
Ram
43k • written 6.7 years ago by
lessismore
★ 1.3k
37
votes
5
replies
13k
views
How do you generate TMM normalized counts using EdgeR?
R
RNA-seq
edgeR
updated 16 days ago by
inedraylig
▴ 60 • written 2.9 years ago by
Pratik
★ 1.0k
34
votes
16
replies
20k
views
9 follow
Filtration Of Reads With Length Lower Than 30 From Bam
read
length
bam
updated 7 days ago by
Hagen
▴ 10 • written 10.2 years ago by
filipzembol
▴ 180
30
votes
12
replies
3.8k
views
Trying to understand the maths behind one Limma function
limma
RNA-Seq
batch-effect
updated 11 days ago by
Ram
43k • written 4.0 years ago by
Mozart
▴ 330
25
votes
11
replies
3.7k
views
6 follow
Forum:
Site Use Guidelines
meta
biostars
Guidelines
updated 3 days ago by
Ram
43k • written 14.6 years ago by
Istvan Albert
100k
23
votes
11
replies
4.8k
views
7 follow
Code golf: detecting homopolymers of length N in the (human) genome
code golf
fasta
homopolymer
repeat
updated 10 days ago by
Ram
43k • written 5.0 years ago by
WouterDeCoster
47k
23
votes
23
replies
9.8k
views
6 follow
How to see if adjusting batch effect in RNA-seq is working or not
RNA-Seq
removeBatchEffect
batch-effect
edger
updated 9 days ago by
Ram
43k • written 5.3 years ago by
iraia.munoa
▴ 130
22
votes
18
replies
6.1k
views
about batch correction in scRNA-seq
scRNA
scRNA-seq
batch-effect
updated 8 days ago by
Ram
43k • written 4.6 years ago by
Bogdan
★ 1.4k
22
votes
14
replies
28k
views
7 follow
removing batch effects using ComBat and SVA
SVA
ComBat
R
Batch-effect
updated 18 days ago by
Ram
43k • written 7.9 years ago by
LJ
▴ 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 6 hours ago by
cmdcolin
★ 3.8k • written 10.8 years ago by
J.F.Jiang
▴ 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 17 days ago by
Ram
43k • written 7.5 years ago by
morteza.mahmoudisaber
▴ 80
17
votes
8
replies
12k
views
9 follow
MAF vs VAF
sequencing
updated 23 days ago by
AshleeThomson
▴ 80 • written 6.1 years ago by
lauren.wahyudi
▴ 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 23 days ago by
Madeleine
• 0 • written 9.8 years ago by
jon.brate
▴ 310
16
votes
10
replies
1.0k
views
6 follow
Forum:
F*up Night style events for Bioinformatics ? Comment if you're interested!
mistakes
updated 28 days ago by
Madelaine Gogol
5.3k • written 29 days ago by
Ann
★ 2.4k
15
votes
6
replies
1.3k
views
6 follow
VCF to human friendly form?
vcf
visualization
updated 11 days ago by
Pierre Lindenbaum
161k • written 19 months ago by
wormball
▴ 10
14
votes
2
replies
7.0k
views
Trouble with Pilon installation
polishing
pilon
installation
updated 1 day ago by
Lissa Cruz Saavedra
• 0 • written 7.3 years ago by
Rox
★ 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 9 days ago by
Ram
43k • written 6.8 years ago by
lessismore
★ 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 17 days ago by
Ram
43k • written 5.7 years ago by
ucakhnd
▴ 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 18 days ago by
ummeswaiba
• 0 • written 10.3 years ago by
biostar
▴ 170
12
votes
17
replies
6.0k
views
9 follow
ACMG assignment tools
wes
acmg
WES
WGS
updated 22 days ago by
Zuber
• 0 • written 3.9 years ago by
Eugene A
▴ 180
12
votes
2
replies
443
views
News:
8th Berlin Summer School in NGS Data Analysis (June 10-14, 2024) - already half booked
Workshop
RNA-Seq
DNA-Seq
Illumina
16 days ago by
David Langenberger
11k
12
votes
4
replies
2.3k
views
long read + salmon? (transcript abundance)
long-read
salmon
updated 21 days ago by
Ram
43k • written 14 months ago by
shinyjj
▴ 50
12
votes
13
replies
4.4k
views
RNA-Seq DGE using PCA components as covariate
differential-gene-expression
RNA-Seq
glm
DESeq2
updated 17 days ago by
Ram
43k • written 6.2 years ago by
firestar
★ 1.6k
11
votes
12
replies
946
views
Downloaded pdb's on rcsb.org
rcsb
pdb
updated 7 days ago by
Ram
43k • written 8 days ago by
iamsmor
• 0
11
votes
9
replies
6.9k
views
How to choose method to integrate different patient sample together in Seurat
Seurat
scRNA
batch-effect
harmony
updated 9 days ago by
Ram
43k • written 4.2 years ago by
623202215
▴ 80
11
votes
6
replies
521
views
Pangenome of plant
pangenome
plant
18 days ago by
analyst
▴ 30
11
votes
9
replies
11k
views
10 follow
Genome assembly statistical tools
Assembly
statistics
updated 13 days ago by
skdv2522
• 0 • written 4.7 years ago by
margab
▴ 10
11
votes
11
replies
1.1k
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 17 days ago by
GenoMax
141k • written 20 days ago by
alejandro.mejiam1
▴ 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 17 days ago by
Ram
43k • written 5.0 years ago by
RNAseqer
▴ 260
10
votes
6
replies
9.8k
views
6 follow
CDS vs cDNA vs transcript for mapping RNA-Seq reads
Assembly
rna-seq
alignment
updated 11 hours ago by
Antonio R. Franco
★ 5.1k • written 6.0 years ago by
williamsbrian5064
▴ 510
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 9 days ago by
Ram
43k • written 5.7 years ago by
Kristin Muench
▴ 620
10
votes
37
replies
12k
views
21 follow
Convert Gene IDs of Tomato Sol Database
tomato
gene
updated 16 days ago by
aziz.hammou
• 0 • written 8.8 years ago by
kevluv93
▴ 170
10
votes
7
replies
7.1k
views
6 follow
Convert GVF to VCF
vcf
updated 10 days ago by
george-hall-ucl
• 0 • written 9.2 years ago by
win
▴ 970
10
votes
5
replies
1.4k
views
6 follow
Courses in RNAseq data
RNA-seq
Courses
updated 24 days ago by
Ram
43k • written 2.5 years ago by
margot.27.muller
▴ 30
10
votes
6
replies
14k
views
7 follow
How To Identify The 16S Rrna Gene Sequence In A Genome
updated 8 days ago by
colindaven
6.4k • written 10.9 years ago by
Ontheway
▴ 10
9
votes
4
replies
271
views
Ubuntu storage space is decreasing automatically
ubuntu
storage
updated 17 days ago by
colindaven
6.4k • written 17 days ago by
analyst
▴ 30
9
votes
4
replies
1.9k
views
Integration of RNA-Seq data with microarray data
microarray
RNA-Seq
batch-effect
R
updated 9 days ago by
Ram
43k • written 4.0 years ago by
Fahimeh.6868
▴ 30
9
votes
10
replies
4.4k
views
Using rnaseq reference sample across batches
RNA-Seq
batch-effect
updated 9 days ago by
Ram
43k • written 7.4 years ago by
denalitastic
▴ 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 8 days ago by
Ram
43k • written 4.5 years ago by
Lucy
▴ 140
9
votes
8
replies
5.6k
views
7 follow
CONTRA for CNV detection. troubleshooting
genome
next-gen-sequencing
cnv
software-error
updated 29 days ago by
Ram
43k • written 9.9 years ago by
Kizuna
▴ 870
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 24 days ago by
Ram
43k • written 16 months ago by
O.rka
▴ 710
1,000 results • Page
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Answer: Trimming tools - your experience please?
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You need to be clear about how `Seurat` defines highly variable genes here. Highly variable genes are the genes that have very high express…
Comment: Heatmap and rna-seq
by
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141k
Please include a link when you are recommending a tool. There can be programs with similar names.
Answer: Heatmap and rna-seq
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Check out clustergrammer from Avi Ma'ayan's lab.
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix
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Simple: ```r data <- lapply(files, read_tsv) data <- Reduce(merge, data) # or Reduce(full_join, data) ``` <a href="" title="Text added bec…
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BioinfGuru
★ 1.7k
Hi, Just thought I'd share this code snippet here for when each file contains multiple samples. I tried using lapply (as suggested by Ram)…
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19k
Take your STAR alignment and sum all the counts for each gene. You can either do this by providing an annotation to STAR, or by running fea…
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If you run your data with plink 2.0, you will have ERRCODE column in your result file showing the reason behind "NA" p-value. https://www.b…
Comment: genome assembly records not present in assembly_summary.txt
by
sapuizait
▴ 10
jesus its in the Genbank file and I was looking at the refseq! I m such a moron - thanks for pointing it out -sorry about that :(
Comment: ScRNA data question
by
bk11
★ 2.4k
I wonder how the `Vlnplots` will look if you normalize the data using `NormalizeData()` function in `Seurat`. The flat line in your plot ar…
Comment: Low mapping rate with Salmon
by
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141k
> Does that mean that the reads that are not mapped to my trascriptome are not exons/coding genes? Reads are likely aligning in regions wh…
Comment: How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
by
cmdcolin
★ 3.8k
the gencode link is broken now but here is a back up of that blogpost on archive https://web.archive.org/web/20130618221342/http://gencodeg…
Comment: Low mapping rate with Salmon
by
Patadu94
• 0
I'll try to make the decoy file again but I remember you also told me that it is only recommended and not mandatory for running `salmon`. I…
Comment: Low mapping rate with Salmon
by
Patadu94
• 0
For doing this, should I just look at the log.out.file?
Answer: Heatmap and rna-seq
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pinheirofabiano
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install.packages("pheatmap") library(pheatmap) setwd("/Users/data_analysis/results") data <- read.table(file…
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