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1,158 results • Page
1 of 24
Sort: Views
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Views
Votes
Replies
362
votes
82
replies
144k
views
35 follow
Tool:
Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
parallel
next-gen
ngs
updated 29 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 27 days ago by
Ram
43k • written 12.8 years ago by
Panos
★ 1.8k
98
votes
106
replies
46k
views
26 follow
Tutorial:
Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
1000genomes
PLINK
PCA
updated 16 days ago by
psb7
▴ 20 • written 5.7 years ago by
Kevin Blighe
87k
39
votes
9
replies
42k
views
6 follow
Batch effects : ComBat or removebatcheffects (limma package) ?
limma
sva
Combat
batch-effect
updated 8 days ago by
Ram
43k • written 6.7 years ago by
lessismore
★ 1.3k
103
votes
42
replies
31k
views
34 follow
Forum:
List of cloud genomics companies
cloud-genomics
updated 16 days ago by
Jeremy Leipzig
22k • written 10.4 years ago by
14134125465346445
★ 3.6k
57
votes
22
replies
28k
views
7 follow
Batch correction in DESeq2
Combat
DESeq2
Batch-Effect
updated 19 days ago by
Ram
43k • written 4.5 years ago by
Arindam Ghosh
▴ 510
22
votes
14
replies
28k
views
7 follow
removing batch effects using ComBat and SVA
SVA
ComBat
R
Batch-effect
updated 16 days ago by
Ram
43k • written 7.9 years ago by
LJ
▴ 280
54
votes
12
replies
28k
views
12 follow
Out Of Disk Space With Picard Tools ?
picard
updated 6 days ago by
kjngo
• 0 • written 12.0 years ago by
Gabriel R.
★ 2.9k
87
votes
24
replies
23k
views
17 follow
Tutorial:
Gene Set Enrichment Analysis
microarray
enrichment
RNA-Seq
GSEA
updated 7 days ago by
Gordon
• 0 • written 3.5 years ago by
Hamid Ghaedi
3.2k
34
votes
16
replies
20k
views
9 follow
Filtration Of Reads With Length Lower Than 30 From Bam
read
length
bam
updated 5 days ago by
Hagen
▴ 10 • written 10.2 years ago by
filipzembol
▴ 180
81
votes
27
replies
20k
views
12 follow
ATAC-seq sample normalization
ChIP-Seq
atac-seq
normalization
updated 21 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
3 hours ago by
Kevin Blighe
87k
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 16 days ago by
ummeswaiba
• 0 • written 10.3 years ago by
biostar
▴ 170
1
vote
7
replies
15k
views
7 follow
How To Annotate Methylation 450K?
methylation
updated 20 days ago by
Vassilis
• 0 • written 10.1 years ago by
liu4gre
▴ 210
17
votes
16
replies
14k
views
10 follow
How to extract the longest isoform from multi fasta file
perl
extract
fasta
python
isoform
updated 21 days ago by
Madeleine
• 0 • written 9.7 years ago by
jon.brate
▴ 310
4
votes
4
replies
14k
views
Heatmap with custom gene labels annotated on the rows
differential-gene-expression
RNAseq
heatmap
updated 15 days ago by
Ram
43k • written 4.7 years ago by
bioinforesearchquestions
▴ 370
10
votes
6
replies
14k
views
7 follow
How To Identify The 16S Rrna Gene Sequence In A Genome
updated 6 days ago by
colindaven
6.4k • written 10.9 years ago by
Ontheway
▴ 10
37
votes
5
replies
13k
views
How do you generate TMM normalized counts using EdgeR?
R
RNA-seq
edgeR
updated 14 days ago by
inedraylig
▴ 60 • written 2.9 years ago by
Pratik
★ 1.0k
1
vote
4
replies
13k
views
RNA sequencing data batch effect removal
RNA-Seq
batch-effect
updated 6 days ago by
Ram
43k • written 7.4 years ago by
Tenghui Chen
• 0
17
votes
8
replies
12k
views
9 follow
MAF vs VAF
sequencing
updated 21 days ago by
AshleeThomson
▴ 80 • written 6.1 years ago by
lauren.wahyudi
▴ 50
10
votes
37
replies
12k
views
21 follow
Convert Gene IDs of Tomato Sol Database
tomato
gene
updated 14 days ago by
aziz.hammou
• 0 • written 8.8 years ago by
kevluv93
▴ 170
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 27 days ago by
Istvan Albert
100k • written 8.1 years ago by
Ram
43k
11
votes
9
replies
11k
views
10 follow
Genome assembly statistical tools
Assembly
statistics
updated 11 days ago by
skdv2522
• 0 • written 4.7 years ago by
margab
▴ 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 8 days ago by
Ram
43k • written 6.8 years ago by
lessismore
★ 1.3k
3
votes
6
replies
11k
views
List of species in RepeatMasker Tool (species parameter)
RepeatMasker
Masking
updated 8 days ago by
Bioinfotec
▴ 10 • written 7.6 years ago by
nut_B
▴ 10
2
votes
5
replies
10k
views
Find Corresponding Author: Doi Metadata?
updated 3 days ago by
Ram
43k • written 10.6 years ago by
Louis
▴ 150
4
votes
3
replies
10k
views
short and long reads
long-reads
Assembly
short-reads
updated 19 days ago by
Ram
43k • written 9.9 years ago by
midox
▴ 290
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 7 days ago by
Ram
43k • written 5.3 years ago by
iraia.munoa
▴ 130
5
votes
13
replies
9.1k
views
8 follow
biomaRt: Timeout on getBM().
r
biomart
ensembl
updated 13 days ago by
Mike Smith
★ 2.0k • written 2.8 years ago by
lincaijin1994
▴ 40
3
votes
10
replies
8.5k
views
6 follow
GATK HaolotypeCaller takes too much time for variant calling
HaplotypeCaller
GATK
updated 19 days ago by
Ram
43k • written 6.4 years ago by
J.F.Jiang
▴ 910
3
votes
6
replies
8.3k
views
RNA-seq, EdgeR and batch effects
RNA-Seq
removeBatchEffect
edgeR
batch-effect
updated 8 days ago by
Ram
43k • written 9.3 years ago by
Ekarl2
▴ 120
16
votes
10
replies
7.7k
views
6 follow
Intersect multiple BED files
bed
intersect
updated 28 days ago by
Alex Reynolds
35k • written 8.3 years ago by
int11ap1
▴ 470
4
votes
3
replies
7.6k
views
Genotype representation with 0, 1, 2 - what do they mean?
genotype
representation
phasing
imputation
gwas
updated 20 days ago by
far
• 0 • written 5.9 years ago by
Volka
▴ 180
4
votes
3
replies
7.4k
views
How to find/decipher Trimmomatic Output
trimmomatic
RNA-Seq
QC
updated 26 days ago by
Ram
43k • written 8.1 years ago by
nikelle.petrillo
▴ 110
5
votes
6
replies
7.3k
views
scatter plot, aov()
aov
scatter-plot
anova
updated 7 days ago by
Ram
43k • written 3.2 years ago by
Rob
▴ 170
5
votes
5
replies
7.2k
views
Converting scRNA-Seq to Bulk-RNASeq
scRNASeq
bulk-RNASeq
RNA-Seq
single-cell
updated 14 days ago by
veldahan86
• 0 • written 3.8 years ago by
Assa Yeroslaviz
★ 1.8k
10
votes
7
replies
7.1k
views
6 follow
Convert GVF to VCF
vcf
updated 8 days ago by
george-hall-ucl
• 0 • written 9.2 years ago by
win
▴ 970
14
votes
2
replies
7.0k
views
Trouble with Pilon installation
polishing
pilon
installation
updated 6 hours ago by
Lissa Cruz Saavedra
• 0 • written 7.3 years ago by
Rox
★ 1.4k
9
votes
3
replies
6.9k
views
EdgeR-GLMs correcting for batch effects
RNA-Seq
edgeR
Batch-Effect
updated 6 days ago by
Ram
43k • written 9.9 years ago by
Matina
▴ 250
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 7 days ago by
Ram
43k • written 4.2 years ago by
623202215
▴ 80
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 6 days ago by
Ram
43k • written 4.5 years ago by
Lucy
▴ 140
6
votes
17
replies
6.6k
views
Can you add a label key to heatscatter plot in R?
heatscatter
visualization
R
updated 7 days ago by
Ram
43k • written 9.5 years ago by
james.lloyd
▴ 100
0
votes
4
replies
6.5k
views
fastq-dump: command not found, what is wrong?
assembly
sratoolkit
genomics
updated 22 days ago by
spalmer
• 0 • written 2.7 years ago by
BioinfoNoob6
• 0
13
votes
10
replies
6.4k
views
Adjusting for confounding variables in RNA-SEQ Differential Expression Analysis
Differential-Gene-Expression
RNA-Seq
Statistics
updated 15 days ago by
Ram
43k • written 5.7 years ago by
ucakhnd
▴ 40
7
votes
20
replies
6.4k
views
7 follow
Repeat masked gtf files from ensembl
ensembl
RNA-Seq
genome
updated 13 days ago by
e.r.zakiev
▴ 200 • written 4.3 years ago by
kevin.stachelek
▴ 80
3
votes
1
reply
6.2k
views
Normalization before or after merging the samples in Seurat
single-cell
seurat
batch-effect
updated 8 days ago by
Ram
43k • written 3.3 years ago by
fouerghi20
▴ 80
1
vote
3
replies
6.1k
views
Error for converting from gene symbol to Entrez IDs
Entrez-ID
org.Dr.eg.db
updated 8 days ago by
Ram
43k • written 5.5 years ago by
modarzi
▴ 170
22
votes
18
replies
6.1k
views
about batch correction in scRNA-seq
scRNA
scRNA-seq
batch-effect
updated 6 days ago by
Ram
43k • written 4.6 years ago by
Bogdan
★ 1.4k
2
votes
4
replies
6.0k
views
Batch Effect Removal in RNA-Seq Data for DGE & WGCNA. Should I omit any samples according to PCA plots?
Batch-effect
RNA-Seq
R
DESeq2
updated 6 days ago by
Ram
43k • written 7.6 years ago by
gokce.ouz
▴ 70
12
votes
17
replies
6.0k
views
9 follow
ACMG assignment tools
wes
acmg
WES
WGS
updated 20 days ago by
Zuber
• 0 • written 3.9 years ago by
Eugene A
▴ 180
1,158 results • Page
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Recent Votes
Comment: clustalo - align milions of short seq, memory issue
Answer: clustalo - align milions of short seq, memory issue
Comment: downloading genomes in fasta format from accession ids
Comment: PCA plot (Suggestions Needed)
Answer: PCA plot (Suggestions Needed)
PCA plot (Suggestions Needed)
Comment: To get p-values for the TPM
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Comment: PCA plot (Suggestions Needed)
by
swbarnes2
14k
The code you already posted in the bioconductor board had simulated data, and the PCA image is the same.
Answer: Network Alignment
by
Scooter
▴ 280
Unfortunately, it's not working for me either, and the web site doesn't exist anymore. You might try reaching out to the authors, but I kn…
Answer: How could I generate a gi_taxid_nucl.dmp file similar to the one previously host
by
ZhangYuanfeng
• 0
JUST GIVE THE ANSWER! Here is the solution: ```bash aria2c -c -s 4 -j 4 \ https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/pd…
Comment: PCA plot (Suggestions Needed)
by
Aaliya
▴ 10
I have actually used DESeq2 data.
Comment: Why cd-hit-est not work when sequence identity threshold<0.95?
by
Dateline
• 0
So, why? I have 18GB of data, and when -c=0.95, the run ends in about two days, while when -c=0.9, it has been three days and only a little…
Answer: Heatmap and rna-seq
by
Kevin Blighe
87k
Hi, you can take the list of GSEA pathways and then use these via GSVA (https://github.com/rcastelo/GSVA) to create a heatmap. You hav…
Comment: Clustering of DAVID gene enrichment results from gene expression studies
by
Kevin Blighe
87k
You will have to elaborate on what is the error
Comment: clustalo - align milions of short seq, memory issue
by
emmanouil.a
▴ 120
Hi GenoMax and Mensur Dlakic, thank you for your feedback. I'm changing approach in the way to work with a smaller number of seq.
Comment: Annovar using R package
by
Pierre Lindenbaum
161k
duplicate of your previous question: https://www.biostars.org/p/9592646/ why using R when there are shell-based tools like VEP ? slivar , …
Comment: Trouble with Pilon installation
by
Lissa Cruz Saavedra
• 0
Hi I am trying to install the software but I didn't find the way to clone from github. Could you help me with the pipeline of instruction…
Comment: Adding CB tag to bam file
by
swbarnes2
14k
I think both these programs are just adding the same tag to every line. I don't think either cares whether it's called RG or CB
Comment: PCA plot (Suggestions Needed)
by
swbarnes2
14k
Even if this was real data, the tiny numbers for the PC1 and PC2 indicate that the differences between the samples are all absolutely tiny.…
Comment: Creating Synthetic Sequences for a ML Model
by
biochugs
• 0
Thanks for the input. I'll continue to think of more ideas that may be achievable.
Comment: PCA plot (Suggestions Needed)
by
Jeremy
▴ 890
You could also try kernel PCA, which is a non-linear form of PCA, although this will be more time-consuming.
Comment: Troubleshooting RNA-seq data with DNA contamination
by
DKA
▴ 40
I have unstranded RNA-seq data. Please share the tool with me, if you do not mind.
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