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1,153 results • Page
1 of 24
Sort: Votes
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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 23 days ago by
jena
▴ 290 • written 11.2 years ago by
ole.tange
★ 4.4k
164
votes
70
replies
60k
views
34 follow
How To Efficiently Parse A Huge Fastq File?
fastq
next-gen-sequencing
updated 21 days ago by
Ram
43k • written 12.8 years ago by
Panos
★ 1.8k
105
votes
15
replies
112k
views
16 follow
Convertion Of Gff3 To Gtf
gtf
gff
updated 29 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 10 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 10 days ago by
psb7
▴ 20 • written 5.6 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 1 day 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 16 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 13 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 18 hours 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 22 days ago by
Istvan Albert
100k • written 8.1 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 2 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 8 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 5 hours ago by
Hagen
▴ 10 • written 10.2 years ago by
filipzembol
▴ 180
31
votes
14
replies
12k
views
11 follow
Finding Rrna Genes In Metagenomic Data
rna
rRNA
metagenomics
updated 24 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 3 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 28 days ago by
Lada
▴ 30 • written 9.4 years ago by
biolab
★ 1.4k
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 2 days ago by
Ram
43k • written 4.9 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 1 day 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 18 hours ago by
Ram
43k • written 4.5 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 10 days ago by
Ram
43k • written 7.9 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 26 days ago by
marshelma
• 0 • written 4.5 years ago by
JJDollar
▴ 130
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 9 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 16 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 16 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 20 days ago by
Madelaine Gogol
5.3k • written 21 days ago by
Ann
★ 2.4k
15
votes
10
replies
7.6k
views
6 follow
Intersect multiple BED files
bed
intersect
updated 22 days ago by
Alex Reynolds
35k • written 8.3 years ago by
int11ap1
▴ 470
15
votes
6
replies
1.2k
views
6 follow
VCF to human friendly form?
vcf
visualization
updated 4 days ago by
Pierre Lindenbaum
161k • written 19 months ago by
wormball
▴ 10
15
votes
6
replies
665
views
Need consultation about my rna-seq workflow
RNA-seq
Gene-expression
updated 28 days ago by
Ram
43k • written 4 weeks 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 2 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 9 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 11 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 15 days ago by
Zuber
• 0 • written 3.9 years ago by
Eugene A
▴ 180
12
votes
2
replies
423
views
News:
8th Berlin Summer School in NGS Data Analysis (June 10-14, 2024) - already half booked
Workshop
RNA-Seq
DNA-Seq
Illumina
9 days ago by
David Langenberger
11k
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
7
replies
6.9k
views
Forum:
Differences between SMART-seq2, SMART-seq3, and 10x
cell
smartseq
UMIs
single
10x
updated 25 days ago by
dsull
★ 5.8k • written 2.6 years ago by
hamarillo
▴ 70
12
votes
4
replies
2.2k
views
long read + salmon? (transcript abundance)
long-read
salmon
updated 13 days ago by
Ram
43k • written 13 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 9 days ago by
Ram
43k • written 6.2 years ago by
firestar
★ 1.6k
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 10 days ago by
GenoMax
141k • written 12 days ago by
alejandro.mejiam1
▴ 10
11
votes
9
replies
11k
views
10 follow
Genome assembly statistical tools
Assembly
statistics
updated 6 days ago by
skdv2522
• 0 • written 4.7 years ago by
margab
▴ 10
11
votes
7
replies
990
views
Shrink logFC values after edgeR
logFC
edgeR
updated 26 days ago by
Gordon Smyth
★ 7.0k • written 11 weeks ago by
arvind.1
▴ 10
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 1 day ago by
Ram
43k • written 4.2 years ago by
623202215
▴ 80
11
votes
8
replies
5.1k
views
Multi-mapping High with featureCounts but not STAR
RNA-Seq
sequencing
alignment
updated 29 days ago by
GenoMax
141k • written 4.9 years ago by
garbuzov
▴ 70
11
votes
12
replies
720
views
Downloaded pdb's on rcsb.org
rcsb
pdb
updated 14 hours ago by
Ram
43k • written 20 hours ago by
iamsmor
• 0
11
votes
6
replies
500
views
Pangenome of plant
pangenome
plant
11 days ago by
analyst
▴ 20
11
votes
22
replies
4.1k
views
No significant DEG: A request to double check my commands for limma.
limma
differential-gene-expression
updated 9 days ago by
Ram
43k • written 5.0 years ago by
RNAseqer
▴ 260
10
votes
37
replies
12k
views
21 follow
Convert Gene IDs of Tomato Sol Database
tomato
gene
updated 9 days ago by
aziz.hammou
• 0 • written 8.8 years ago by
kevluv93
▴ 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 2 days ago by
Ram
43k • written 5.7 years ago by
Kristin Muench
▴ 620
10
votes
7
replies
7.1k
views
6 follow
Convert GVF to VCF
vcf
updated 3 days ago by
george-hall-ucl
• 0 • written 9.2 years ago by
win
▴ 970
10
votes
6
replies
4.1k
views
Tutorial:
CorLevelPlot - Visualise correlation results, e.g., clinical parameter correlations
correlation
corlevelplot
updated 23 days ago by
Ram
43k • written 6.2 years ago by
Kevin Blighe
87k
10
votes
6
replies
14k
views
7 follow
How To Identify The 16S Rrna Gene Sequence In A Genome
updated 22 hours ago by
colindaven
6.3k • written 10.9 years ago by
Ontheway
▴ 10
1,153 results • Page
1 of 24
Recent Votes
Basic normalization, batch correction and visualization of RNA-seq data
A: Read counts of STAR with gff file
Comment: Free/open source 23andme-like analysis
A: How to obtain all accession.version identifiers for a BLAST database using ENTRE
Comment: Editing Human Reference Genome by adding a CDS
Answer: Plink merge errors.
Gene Set Enrichment Analysis
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i.sudbery
19k
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• 0
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54k
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★ 2.0k
Recent Replies
Answer: Plink merge errors.
by
Dinmukhamed
• 0
I found answer https://www.biostars.org/p/101191/.
Comment: Ciriquant not configuring hisat2 indexed files
by
Atul K.
• 0
it worked. Thank you. Now my terminal is crashing, seems 16gb of RAM and 4 cores isn't enough. Can you suggest something?
Comment: Adding CB tag to bam file
by
Maria
• 0
I checked Picard ```AddOrReplaceReadsGroups``` and ```AddOATag```. Is that what you're referring to?
Comment: Free/open source 23andme-like analysis
by
Michael
54k
Noted that 'accurate' wasn't among your criteria ;) Anyway, most variant callers are free open-source software. However, for ancestry ana…
Answer: Mapping cDNA sequence of a single gene to a genome not hosted at UCSC server (wi
by
Pierre Lindenbaum
161k
> server so I cannot use Blat for this purpose. blat is avilable as a standane tool: http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86…
Answer: Mapping cDNA sequence of a single gene to a genome not hosted at UCSC server (wi
by
b.contreras.moreira
▴ 160
My favourite for this task would be [GMAP]( http://research-pub.gene.com/gmap ), which can produce GFF format with option `-f 2`. It is…
Answer: Prediction of Ribosomal RNA Genes Using RNAmmer Software
by
colindaven
6.3k
Another alternative is the truly free implementation barrnap https://github.com/tseemann/barrnap. This is also installable via conda so qui…
Comment: Filtration Of Reads With Length Lower Than 30 From Bam
by
Hagen
▴ 10
thanks! This saved me quite some time, I was about to write code to calculate the aligned length from the CIGAR. But this can be done with …
Comment: Per base sequence content failed miserably
by
Kai Xin
• 0
will look into that. Thank you very much
Comment: Korean human genome reference file
by
SeoGyun
• 0
Thanks..... But I want to do imputation, so I have to make it as a vcf file, but the site only has a fatsa file....
Comment: miRNAs quantification using mirdeep2 tool
by
Ashok
• 0
thank you for your reply https://github.com/rajewsky-lab/mirdeep2/blob/master/TUTORIAL.md i saw this github tutorial for miRNA quantifica…
Comment: Load a full GFF3 into annotation track using arrow (Apollo)
by
cmdcolin
★ 3.8k
Hi there, I let a developer know of this thread and they said they can check it out next week. Feel free to post to the https://github.com/…
Comment: How to get the reference panel for UKBB
by
航太郎
• 0
Thanks for your guide!
Comment: Removing duplicates
by
joe
▴ 510
I'd try those OP @samuel recommends My guess is you're new to ONT, fast5 is the 'raw data' which is current over time...other than generat…
Comment: RNA seq differential expression analysis
by
swbarnes2
14k
No. Find a tutorial, try it, then if you have specific questions, ask of the galaxy help site.
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