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1,103 results • Page
1 of 23
Sort: Views
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
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
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
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
39
votes
9
replies
42k
views
6 follow
Batch effects : ComBat or removebatcheffects (limma package) ?
limma
sva
Combat
batch-effect
updated 1 day 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 9 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 12 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 9 days ago by
Ram
43k • written 7.8 years ago by
LJ
▴ 280
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
85
votes
24
replies
23k
views
17 follow
Tutorial:
Gene Set Enrichment Analysis
microarray
enrichment
RNA-Seq
GSEA
updated 8 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 15 days ago by
sgv
• 0 • written 4.3 years ago by
Flo
▴ 240
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
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
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
1
vote
7
replies
15k
views
7 follow
How To Annotate Methylation 450K?
methylation
updated 13 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 14 days ago by
Madeleine
• 0 • written 9.7 years ago by
jon.brate
▴ 290
4
votes
4
replies
14k
views
Heatmap with custom gene labels annotated on the rows
differential-gene-expression
RNAseq
heatmap
updated 8 days ago by
Ram
43k • written 4.7 years ago by
bioinforesearchquestions
▴ 370
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
17
votes
8
replies
12k
views
9 follow
MAF vs VAF
sequencing
updated 15 days ago by
AshleeThomson
▴ 70 • 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 8 days ago by
aziz.hammou
• 0 • written 8.8 years ago by
kevluv93
▴ 170
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
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
11
votes
9
replies
11k
views
10 follow
Genome assembly statistical tools
Assembly
statistics
updated 5 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 1 day ago by
Ram
43k • written 6.8 years ago by
lessismore
★ 1.3k
3
votes
6
replies
10k
views
List of species in RepeatMasker Tool (species parameter)
RepeatMasker
Masking
updated 1 day ago by
Bioinfotec
▴ 10 • written 7.5 years ago by
nut_B
▴ 10
4
votes
3
replies
10k
views
short and long reads
long-reads
Assembly
short-reads
updated 12 days ago by
Ram
43k • written 9.9 years ago by
midox
▴ 290
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 16 hours ago by
Ram
43k • written 5.3 years ago by
iraia.munoa
▴ 130
5
votes
13
replies
9.0k
views
8 follow
biomaRt: Timeout on getBM().
r
biomart
ensembl
updated 6 days ago by
Mike Smith
★ 2.0k • written 2.8 years ago by
lincaijin1994
▴ 40
3
votes
10
replies
8.4k
views
6 follow
GATK HaolotypeCaller takes too much time for variant calling
HaplotypeCaller
GATK
updated 12 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 1 day ago by
Ram
43k • written 9.3 years ago by
Ekarl2
▴ 120
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
4
votes
3
replies
7.5k
views
Genotype representation with 0, 1, 2 - what do they mean?
genotype
representation
phasing
imputation
gwas
updated 13 days ago by
far
• 0 • written 5.9 years ago by
Volka
▴ 180
4
votes
3
replies
7.3k
views
How to find/decipher Trimmomatic Output
trimmomatic
RNA-Seq
QC
updated 19 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 1 day ago by
Ram
43k • written 3.1 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 7 days ago by
veldahan86
• 0 • written 3.8 years ago by
Assa Yeroslaviz
★ 1.8k
10
votes
7
replies
7.0k
views
6 follow
Convert GVF to VCF
vcf
updated 2 days ago by
george-hall-ucl
• 0 • written 9.2 years ago by
win
▴ 970
12
votes
7
replies
6.9k
views
Forum:
Differences between SMART-seq2, SMART-seq3, and 10x
cell
smartseq
UMIs
single
10x
updated 24 days ago by
dsull
★ 5.8k • written 2.6 years ago by
hamarillo
▴ 70
8
votes
7
replies
6.9k
views
Parse the Xml response from Entrez Db=bioproject Using Biopython eFetch
entrez
efetch
biopython
xml
updated 28 days ago by
LauferVA
4.2k • written 8.9 years ago by
Prasad
▴ 50
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 16 hours ago by
Ram
43k • written 4.2 years ago by
623202215
▴ 80
6
votes
17
replies
6.5k
views
Can you add a label key to heatscatter plot in R?
heatscatter
visualization
R
updated 1 day ago by
Ram
43k • written 9.5 years ago by
james.lloyd
▴ 100
0
votes
4
replies
6.4k
views
fastq-dump: command not found, what is wrong?
assembly
sratoolkit
genomics
updated 15 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 8 days ago by
Ram
43k • written 5.7 years ago by
ucakhnd
▴ 40
7
votes
20
replies
6.3k
views
7 follow
Repeat masked gtf files from ensembl
ensembl
RNA-Seq
genome
updated 6 days ago by
e.r.zakiev
▴ 190 • written 4.3 years ago by
kevin.stachelek
▴ 80
3
votes
1
reply
6.1k
views
Normalization before or after merging the samples in Seurat
single-cell
seurat
batch-effect
updated 1 day 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 1 day ago by
Ram
43k • written 5.5 years ago by
modarzi
▴ 160
12
votes
17
replies
6.0k
views
9 follow
ACMG assignment tools
wes
acmg
WES
WGS
updated 14 days ago by
Zuber
• 0 • written 3.9 years ago by
Eugene A
▴ 180
0
votes
7
replies
6.0k
views
Pre-processing of RNA-Seq data for WGCNA
RNA-Seq
WGCNA
removeBatchEffect
DESeq2
updated 1 day ago by
Ram
43k • written 7.6 years ago by
gokce.ouz
▴ 70
3
votes
11
replies
5.9k
views
Modifying R pairs() function
plotMEpairs
WGCNA
R
updated 1 day ago by
Ram
43k • written 6.4 years ago by
shania90.lk
▴ 30
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 1 day ago by
Ram
43k • written 5.7 years ago by
Kristin Muench
▴ 620
1,103 results • Page
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Comment: Indexing the Reference Genome is not done in STAR
by
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• 0
I add these parameters; #SBATCH -N 4 #SBATCH --tasks=1 #SBATCH -c 4 #SBATCH --time=24:00:00 But it keeps giving error
Comment: RNA seq differential expression analysis
by
rrehimi
• 0
Thanks! Could you please explain the DEseq2 method using Galaxy step by step? Input files?
Answer: Korean reference file
by
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6.3k
Is is this one - KOREF ? There might be multiple versions. https://www.ncbi.nlm.nih.gov/bioproject/PRJNA294231/ If it is, then take that…
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by
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The question is not quite clear? are you asking for wheat proteins in UniProtKB which contain a lysine amino-acid, where those lysine are *…
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by
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★ 1.9k
You should provide row count (without normalization) for doing DEG analysis by relevant tools such as, edgeR or DEseq.
Comment: GSEA analysis in R
by
Sudip
• 0
Thank you. I have another question. Is there a way to get the gene list under "setSize" from the output that you gave as an example.
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by
Kai Xin
• 0
Hi, i have added the fastqc plots (untrimmed and trimmed). The sample was from anaerobes enriched from wastewater treatment plant, and this…
Comment: How can I retrieve wheat lysine non-acetylated sequences from the UniProt databa
by
Pierre Lindenbaum
161k
> lysine non-acetylated sequences what does it look like in uniprot ? give us an example with a uniprot identifier.
Answer: Indexing the Reference Genome is not done in STAR
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Pierre Lindenbaum
161k
> CPU time limit exceeded your command is taking too long and can't be completed. check your cluster documentation to allocate more …
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by
quentinperriere
• 0
thank you for responding. I was looking for suitable variant calling tool. I'm working on fungus and I don't have fast5 files. Could you re…
Comment: How to reduce the variation of CIBERSORTx results?
by
feather-W
• 0
Hi LChart, Thanks for your reply. I see S-mode in the CIBERSORTx official website tutorial(https://cibersortx.stanford.edu/), and the imag…
Comment: How to reduce the variation of CIBERSORTx results?
by
LChart
3.9k
First time I've heard of S-mode. I imagine you've seen this benchmark where it doesn't come out too well: https://academic.oup.com/bib/arti…
Comment: ISCN annotation for SV/CN VCF files
by
adedare
• 0
https://res.saletool.cn/vcf/18084521725806
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.
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