Latest
Open
Jobs
Tutorials
Tags
About
FAQ
Community
Planet
New Post
Log In
New Post
Latest
Open
News
Jobs
Tutorials
Forum
Tags
Planet
Users
Log In
Sign Up
About
Limit : this month
all time
today
this week
this month
this year
1,000 results • Page
1 of 20
Sort: Votes
Rank
Views
Votes
Replies
362
votes
82
replies
143k
views
35 follow
Tool:
Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
parallel
next-gen
ngs
updated 22 days ago by
jena
▴ 290 • written 11.2 years ago by
ole.tange
★ 4.4k
185
votes
44
replies
83k
views
30 follow
Drawing Chromosome Ideograms With Data
ideogram
visualization
chromosome
updated 29 days ago by
Michael
54k • written 14.1 years ago by
Yuri
★ 1.7k
164
votes
70
replies
60k
views
34 follow
How To Efficiently Parse A Huge Fastq File?
fastq
next-gen-sequencing
updated 20 days ago by
Ram
43k • written 12.8 years ago by
Panos
★ 1.8k
105
votes
15
replies
111k
views
16 follow
Convertion Of Gff3 To Gtf
gtf
gff
updated 28 days ago by
xiaoleiusc
▴ 140 • written 11.9 years ago by
GouthamAtla
12k
103
votes
42
replies
31k
views
34 follow
Forum:
List of cloud genomics companies
cloud-genomics
updated 9 days ago by
Jeremy Leipzig
22k • written 10.4 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 9 days ago by
psb7
▴ 20 • written 5.6 years ago by
Kevin Blighe
87k
85
votes
24
replies
23k
views
17 follow
Tutorial:
Gene Set Enrichment Analysis
microarray
enrichment
RNA-Seq
GSEA
updated 2 hours 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 14 days ago by
sgv
• 0 • written 4.3 years ago by
Flo
▴ 240
57
votes
22
replies
28k
views
7 follow
Batch correction in DESeq2
Combat
DESeq2
Batch-Effect
updated 12 days ago by
Ram
43k • written 4.5 years ago by
Arindam Ghosh
▴ 510
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 20 days ago by
Istvan Albert
100k • written 8.1 years ago by
Ram
43k
47
votes
15
replies
16k
views
10 follow
DESeq2 compare all levels
differential-gene-expression
RNA-Seq
DESeq2
updated 29 days ago by
Bionaught
• 0 • written 5.8 years ago by
firestar
★ 1.6k
39
votes
9
replies
42k
views
6 follow
Batch effects : ComBat or removebatcheffects (limma package) ?
limma
sva
Combat
batch-effect
updated 23 hours 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 7 days ago by
inedraylig
▴ 60 • written 2.8 years ago by
Pratik
★ 1.0k
34
votes
16
replies
20k
views
14 follow
Tutorial:
TCGA UUIDS to TCGA barcode (SampleID) in R
next-gen
GDC
R
TCGA
updated 29 days ago by
aUser
▴ 30 • written 7.5 years ago by
martinguerrerog89
▴ 310
31
votes
14
replies
12k
views
11 follow
Finding Rrna Genes In Metagenomic Data
rna
rRNA
metagenomics
updated 23 days ago by
Ram
43k • written 13.5 years ago by
toshnam
▴ 650
30
votes
12
replies
3.8k
views
Trying to understand the maths behind one Limma function
limma
RNA-Seq
batch-effect
updated 2 days ago by
Ram
43k • written 4.0 years ago by
Mozart
▴ 330
26
votes
5
replies
23k
views
BLAST options: max_target_seqs and num_alignments
blast
updated 27 days ago by
Lada
▴ 30 • written 9.4 years ago by
biolab
★ 1.4k
23
votes
23
replies
9.7k
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 hours ago by
Ram
43k • written 5.3 years ago by
iraia.munoa
▴ 130
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 1 day ago by
Ram
43k • written 4.9 years ago by
WouterDeCoster
47k
22
votes
14
replies
28k
views
7 follow
removing batch effects using ComBat and SVA
SVA
ComBat
R
Batch-effect
updated 9 days ago by
Ram
43k • written 7.8 years ago by
LJ
▴ 280
21
votes
6
replies
16k
views
survfit(Surv()) P-value interpretation for 3 survival curves?
survfit
Surv
survival curves
R
updated 25 days ago by
marshelma
• 0 • written 4.5 years ago by
JJDollar
▴ 130
18
votes
20
replies
4.3k
views
6 follow
How to identify significant differentially expressed genes and gene regulatory networks from microarray data.
microarray
differential-gene-expression
updated 8 days ago by
Ram
43k • written 7.5 years ago by
morteza.mahmoudisaber
▴ 80
17
votes
16
replies
14k
views
10 follow
How to extract the longest isoform from multi fasta file
perl
extract
fasta
python
isoform
updated 14 days ago by
Madeleine
• 0 • written 9.7 years ago by
jon.brate
▴ 290
17
votes
8
replies
12k
views
9 follow
MAF vs VAF
sequencing
updated 14 days ago by
AshleeThomson
▴ 70 • written 6.1 years ago by
lauren.wahyudi
▴ 50
16
votes
10
replies
1.0k
views
6 follow
Forum:
F*up Night style events for Bioinformatics ? Comment if you're interested!
mistakes
updated 19 days ago by
Madelaine Gogol
5.3k • written 20 days ago by
Ann
★ 2.4k
15
votes
6
replies
1.2k
views
6 follow
VCF to human friendly form?
vcf
visualization
updated 2 days ago by
Pierre Lindenbaum
161k • written 19 months ago by
wormball
▴ 10
15
votes
10
replies
7.6k
views
6 follow
Intersect multiple BED files
bed
intersect
updated 21 days ago by
Alex Reynolds
35k • written 8.3 years ago by
int11ap1
▴ 470
15
votes
6
replies
655
views
Need consultation about my rna-seq workflow
RNA-seq
Gene-expression
updated 27 days ago by
Ram
43k • written 29 days ago by
markusz
▴ 10
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 23 hours ago by
Ram
43k • written 6.8 years ago by
lessismore
★ 1.3k
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 9 days ago by
ummeswaiba
• 0 • written 10.3 years ago by
biostar
▴ 170
13
votes
10
replies
6.4k
views
Adjusting for confounding variables in RNA-SEQ Differential Expression Analysis
Differential-Gene-Expression
RNA-Seq
Statistics
updated 8 days ago by
Ram
43k • written 5.7 years ago by
ucakhnd
▴ 40
12
votes
14
replies
2.4k
views
8 follow
Forum:
Recovering bam files after unknown deletion in the storage
photorec
bam
sequencing
written 4.9 years ago by
Gabriel Wajnberg
▴ 70
12
votes
13
replies
4.3k
views
RNA-Seq DGE using PCA components as covariate
differential-gene-expression
RNA-Seq
glm
DESeq2
updated 8 days ago by
Ram
43k • written 6.2 years ago by
firestar
★ 1.6k
12
votes
2
replies
420
views
News:
8th Berlin Summer School in NGS Data Analysis (June 10-14, 2024) - already half booked
Workshop
RNA-Seq
DNA-Seq
Illumina
7 days ago by
David Langenberger
11k
12
votes
17
replies
6.0k
views
9 follow
ACMG assignment tools
wes
acmg
WES
WGS
updated 13 days ago by
Zuber
• 0 • written 3.9 years ago by
Eugene A
▴ 180
12
votes
7
replies
6.9k
views
Forum:
Differences between SMART-seq2, SMART-seq3, and 10x
cell
smartseq
UMIs
single
10x
updated 23 days ago by
dsull
★ 5.8k • written 2.6 years ago by
hamarillo
▴ 70
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 10 hours ago by
Ram
43k • written 4.2 years ago by
623202215
▴ 80
11
votes
7
replies
980
views
Shrink logFC values after edgeR
logFC
edgeR
updated 25 days ago by
Gordon Smyth
★ 7.0k • written 10 weeks ago by
arvind.1
▴ 10
11
votes
22
replies
4.1k
views
No significant DEG: A request to double check my commands for limma.
limma
differential-gene-expression
updated 8 days ago by
Ram
43k • written 5.0 years ago by
RNAseqer
▴ 260
11
votes
9
replies
11k
views
10 follow
Genome assembly statistical tools
Assembly
statistics
updated 4 days ago by
skdv2522
• 0 • written 4.7 years ago by
margab
▴ 10
11
votes
8
replies
5.1k
views
Multi-mapping High with featureCounts but not STAR
RNA-Seq
sequencing
alignment
updated 28 days ago by
GenoMax
141k • written 4.9 years ago by
garbuzov
▴ 70
11
votes
6
replies
495
views
Pangenome of plant
pangenome
plant
9 days ago by
analyst
▴ 20
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 8 days ago by
GenoMax
141k • written 11 days ago by
alejandro.mejiam1
▴ 10
11
votes
4
replies
2.2k
views
long read + salmon? (transcript abundance)
long-read
salmon
updated 12 days ago by
Ram
43k • written 13 months ago by
shinyjj
▴ 50
10
votes
37
replies
12k
views
21 follow
Convert Gene IDs of Tomato Sol Database
tomato
gene
updated 7 days ago by
aziz.hammou
• 0 • written 8.8 years ago by
kevluv93
▴ 170
10
votes
6
replies
4.1k
views
Tutorial:
CorLevelPlot - Visualise correlation results, e.g., clinical parameter correlations
correlation
corlevelplot
updated 22 days ago by
Ram
43k • written 6.2 years ago by
Kevin Blighe
87k
10
votes
36
replies
5.7k
views
Design in DESeq: Can you combine explicit and implicit batch effect correction in (SVA+Metadata Variables)?
SVA
batch-effect
DESeq2
R
updated 23 hours ago by
Ram
43k • written 5.7 years ago by
Kristin Muench
▴ 620
10
votes
7
replies
7.0k
views
6 follow
Convert GVF to VCF
vcf
updated 1 day 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 15 days ago by
Ram
43k • written 2.5 years ago by
margot.27.muller
▴ 30
9
votes
5
replies
2.2k
views
Millions of Reads Needed for Differential Gene Expression
differential-gene-expression
RNA-Seq
deseq2
updated 8 days ago by
Ram
43k • written 4.6 years ago by
contact
▴ 20
1,000 results • Page
1 of 20
Recent Votes
High fold change values
C: Bcftools Mpileup Removes Marked Duplicates?
Prediction tools summary - zero values
A: Error with Formatdb of legacy blast?
Error with Formatdb of legacy blast?
Answer: How to convert SAM/BAM file to GTF/GFF file?
A: Ribo-seq vs RNA-seq read count
Recent Locations •
All
South Korea,
just now
Hong Kong,
just now
Palau,
1 minute ago
United States,
11 minutes ago
United States,
14 minutes ago
Toronto,
23 minutes ago
United States,
25 minutes ago
Recent Awards •
All
Popular Question
to
Yingying
• 0
Popular Question
to
anasjamshed
▴ 120
Popular Question
to
synat.keam
▴ 100
Popular Question
to
Rui
▴ 50
Popular Question
to
otieno43
▴ 20
Scholar
to
bk11
★ 2.3k
Popular Question
to
jammydodger123456
▴ 40
Recent Replies
Comment: ISCN annotation for SV/CN VCF files
by
adedare
• 0
https://res.saletool.cn/vcf/18084435127462
Comment: How can I solve this error?
by
22211020193
• 0
I want to conduct GWAS meta-analysis using metal software.
Comment: How to reduce the variation of CIBERSORTx results?
by
feather-W
• 0
Hi LChart, Thanks for your reply. Yes, the identical command lines produce different results in CIBERSORTx S-mode. Although I input the da…
Comment: Removing duplicates
by
joe
▴ 490
I *could* imagine an ONT scenario where you'd want to remove duplicates (amplicon-seq, etc) but likely for variant calling there is no need…
Comment: Removing duplicates
by
samuel.a.odonnell
▴ 510
As above, you do not need to worry about duplicates for ONT data Also have you looked at using other tools for variant calling more suited…
Answer: Pediococcus acidilactici sequence analysis
by
geneontologyhelp
▴ 340
If you're looking for the GO annotations for *Pediococcus acidilactici*, these are available. Using the instructions under [*2. All other…
Answer: What is the normalization status of metabric data?
by
etiennedanis
▴ 10
I just found an answer to this question here: [https://groups.google.com/g/cbioportal/c/hm_i4jbG1uc/m/h9rNYOvpAAAJ][1] [1]: https://gro…
Comment: Removing duplicates
by
joe
▴ 490
With ONT you will only have PCR duplicates. 'Read' (you mean optical?) duplicates are an artifact of cluster-based sequencing (ie Illumina)…
Comment: assembly using CCS, CLR, CCS_CLR sequences together?
by
GenoMax
141k
PacBio has some recommendations on software for genome assemblies on this page (which you may have seen but just in case): https://www.pacb…
Answer: DEG analysis of RNA-seq data across multiple tissues and two conditions
by
swbarnes2
14k
I would not put totally different tissues in the same DESeq object. I don't think that's going to do good things for normalization or disp…
Comment: Removing duplicates
by
quentinperriere
• 0
pcr duplicates or/and read duplicates should I use this command to remove them ? or we don't talk about duplicates when dealing with ONT ??…
Comment: How to reduce the variation of CIBERSORTx results?
by
LChart
3.9k
If you didn't change the input signature matrix, the input RNA matrix, or the input parameters - what did you change? Is the statement that…
Answer: Inconsistency in SNP detection pipelines for multi-sample analysis
by
LChart
3.9k
> To replicate GVCF behavior and avoid issues with 0/0 genotypes appearing as missing, I don't use the -v option I'm not sure what you m…
Comment: Supergnova stuck in tutorial
by
GenoMax
141k
Your best option may be to email the author (and/or the senior author from the paper). Let them know that the FTP links mentioned on GitHub…
Comment: DEG analysis of RNA-seq data across multiple tissues and two conditions
by
BioinfGuru
★ 1.7k
Thanks @lchart, I accept that, I'll wait to see if there's any more who want to input and then accept the answer
Traffic: 1965 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