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1,000 results • Page
4 of 20
Sort: Views
Rank
Views
Votes
Replies
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
28
votes
11
replies
19k
views
9 follow
Salary For A Bioinformatics Programmer In Europe?
career
updated 11 months ago by
Ram
43k • written 12.7 years ago by
Jeroen Van Goey
2.3k
24
votes
15
replies
19k
views
7 follow
how can I remove duplicated variants from vcf file?
SNP
vcf
updated 8 months ago by
Ram
43k • written 6.8 years ago by
kk.mahsa
▴ 140
14
votes
17
replies
19k
views
6 follow
HISAT2 command help
RNA-Seq
alignment
updated 3 months ago by
DareDevil
★ 4.3k • written 8.3 years ago by
dina.hesham139
▴ 170
20
votes
16
replies
19k
views
6 follow
Conversion of Gene Name to Ensembl ID
gene
RNA-Seq
R
genome
updated 5 months ago by
Nat.Nataren
▴ 10 • written 4.1 years ago by
bazok
▴ 20
38
votes
21
replies
19k
views
8 follow
Tool:
pybam - 100% python BAM reader
python
htspython
bam
pysam
updated 10 months ago by
Ram
43k • written 8.0 years ago by
John
13k
28
votes
7
replies
19k
views
6 follow
VCF merge or concatenate?
snp
VCF
VCFTools
written 4.8 years ago by
rokragna295
▴ 60
176
votes
46
replies
19k
views
26 follow
Forum:
Crac: Funny And/Or Weird Names For Bioinformatics Tools
humor
5 months ago by
Istvan Albert
100k
8
votes
6
replies
19k
views
Converting gtf format to bed format
bed
updated 4 months ago by
Apex92
▴ 280 • written 9.5 years ago by
thjnant
▴ 160
83
votes
34
replies
19k
views
22 follow
Tutorial:
Enrichment Analysis, Clustering and Scoring with pathfindR
enrichment
R
pathway
active-subnetwork
updated 11 months ago by
adelheidkratzer
• 0 • written 5.8 years ago by
egeulgen
★ 1.3k
26
votes
9
replies
19k
views
8 follow
Favorite Splice Site Prediction/Evaluation Tools
splicing
prediction
updated 10 months ago by
abhilashdasari.10
▴ 30 • written 11.4 years ago by
Alex Paciorkowski
3.5k
15
votes
9
replies
19k
views
8 follow
How to count fasta sequences efficiently using (or not ) biopython
biopython
python
fasta
updated 5 months ago by
Mark
★ 1.5k • written 6.3 years ago by
juan.crescente
▴ 110
38
votes
26
replies
18k
views
16 follow
GO analysis: DAVID vs GREAT vs GOrilla
RNA-Seq
ChIP-Seq
GO
gene ontology
written 8.2 years ago by
biostart
▴ 370
3
votes
8
replies
18k
views
Downloading gtf file for RefSeq
RNA-Seq
RefSeq
GTF
updated 3 months ago by
xiaoleiusc
▴ 140 • written 6.6 years ago by
KVC_bioinfo
▴ 590
13
votes
7
replies
18k
views
Running STAR aligner on paired-end reads as single-end read
RNA-Seq
paired end
single end
STAR
align
updated 4 months ago by
xiaoleiusc
▴ 140 • written 5.7 years ago by
Glory Basumata
▴ 140
6
votes
5
replies
18k
views
7 follow
How different is rlog transformation from vst transformation in DESeq2
DESeq2
count normalization
updated 8 months ago by
ATpoint
82k • written 5.6 years ago by
piyushjo
▴ 700
51
votes
6
replies
18k
views
Decoy In Reference Assembly
1000genomes
updated 11 months ago by
kmzhou4
• 0 • written 10.9 years ago by
Sangwoo Kim
▴ 420
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
38
votes
12
replies
18k
views
8 follow
BEDOPS gtf2bed conversion error with Ensembl GTF
gtf2bed
ensembl
bedops
gtf
updated 8 weeks ago by
Alex Reynolds
35k • written 7.7 years ago by
bioinformatics.cancer
▴ 260
17
votes
10
replies
18k
views
Regarding Split reads and discordant reads
genome
sequence
sequencing
alignment
updated 11 months ago by
Ram
43k • written 6.5 years ago by
DL
▴ 50
1
vote
2
replies
18k
views
Forum:
Would you rather analyze a dataset with a strong, non-collinear batch effect, or a weak, collinear batch effect.
collinear
latent
batch-effect
variable
GLM
9 months ago by
LauferVA
4.2k
6
votes
9
replies
18k
views
HISAT2 software installation
RNA-Seq
updated 11 weeks ago by
GenoMax
141k • written 6.6 years ago by
saj98
▴ 140
12
votes
11
replies
17k
views
Trying to get genome for bedtools
genome
updated 9 months ago by
mg
▴ 250 • written 7.7 years ago by
radwa.raed
▴ 40
21
votes
11
replies
17k
views
the problem with rpkm (and tpm)
RNA-Seq
next-gen
gene-expression
normalization
updated 10 months ago by
Chris
▴ 260 • written 9.5 years ago by
user123456
▴ 180
9
votes
10
replies
17k
views
8 follow
Forum:
Open Source Bioinformatics projects for beginners
Open-Source
Beginners
updated 12 weeks ago by
Saransh
• 0 • written 6.3 years ago by
Eugenia84
▴ 40
65
votes
24
replies
17k
views
14 follow
Mapping Snps To Pathways
snp
genotyping
pathway
gene
enrichment
updated 6 months ago by
Ram
43k • written 14.2 years ago by
Pierre Lindenbaum
161k
8
votes
6
replies
17k
views
News:
Bioinformatics PhD Programs in the US
education
PhD
updated 11 months ago by
Ram
43k • written 6.4 years ago by
Ahmed Youssef
▴ 70
20
votes
10
replies
17k
views
Could you please explain Fold change, % of change, and log2 fold change (L2FC) to a layment?
gene
RNA-Seq
next-gen
fold-change
updated 7 months ago by
Ram
43k • written 4.5 years ago by
WUSCHEL
▴ 750
17
votes
9
replies
17k
views
6 follow
Tool:
ggrepel: repel overlapping text labels in ggplot2
R
visualization
updated 10 months ago by
Ram
43k • written 8.3 years ago by
Kamil
★ 2.3k
3
votes
9
replies
16k
views
8 follow
Module to RMSD two proteins with Python?
python
protein-structure
updated 10 months ago by
Aleksandr
• 0 • written 8.3 years ago by
bef1
• 0
12
votes
11
replies
16k
views
10 follow
Retrieve The Reads And Fastq From Bam File
samtools
updated 6 months ago by
Reem
• 0 • written 11.5 years ago by
rehma.ar
▴ 290
35
votes
17
replies
16k
views
12 follow
Tutorial:
Machine Learning For Cancer Classification - Part 3 - Predicting With A Random Forest Classifier
machine-learning
classification
updated 11 months ago by
GenoMax
141k • written 10.4 years ago by
Obi Griffith
20k
10
votes
8
replies
16k
views
6 follow
Error: Eof Marker Is Absent When Processing A Bam File
samtools
updated 11 months ago by
Ram
43k • written 11.7 years ago by
Mary
▴ 50
27
votes
6
replies
16k
views
Tool:
Bioawk - Fasta, Fastq, Sam, Bed, Gff Aware Awk Programming
awk
updated 10 months ago by
Ram
43k • written 11.8 years ago by
Istvan Albert
100k
21
votes
6
replies
16k
views
survfit(Surv()) P-value interpretation for 3 survival curves?
survfit
Surv
survival curves
R
updated 4 weeks ago by
marshelma
• 0 • written 4.6 years ago by
JJDollar
▴ 130
30
votes
18
replies
16k
views
8 follow
Is It Possible For Two Different Affymetrix Probe Set Id To Have Common Annotations To Same Gene ?
microarray
annotation
affymetrix
probeset
updated 5 months ago by
Ram
43k • written 14.1 years ago by
Khader Shameer
18k
47
votes
15
replies
16k
views
10 follow
DESeq2 compare all levels
differential-gene-expression
RNA-Seq
DESeq2
updated 5 weeks ago by
Bionaught
• 0 • written 5.8 years ago by
firestar
★ 1.6k
7
votes
11
replies
16k
views
11 follow
How to generate KEGG pathway classification chart
RNA-Seq
kegg
updated 9 months ago by
microecologist93
▴ 20 • written 5.1 years ago by
dongchenchen
▴ 30
15
votes
34
replies
16k
views
10 follow
Issues installing bcl2fastq?
bcl2fastq
demultiplexing
updated 7 weeks ago by
barslmn
★ 2.1k • written 6.7 years ago by
a.rex
▴ 350
35
votes
10
replies
16k
views
11 follow
Which Chip Seq Peak Callers Do You Use?
chip-seq
peak-calling
updated 5 months ago by
Ram
43k • written 14.0 years ago by
Stew
★ 1.4k
21
votes
7
replies
16k
views
6 follow
GFA to Fasta file
sequence
updated 3 months ago by
Adam Taranto
▴ 40 • written 8.4 years ago by
marcela.uliano
▴ 90
7
votes
14
replies
16k
views
7 follow
Tool:
Art: Simulation Tools To Generate Synthetic Next-Generation Sequencing Reads.
sequence
updated 10 months ago by
Ram
43k • written 11.8 years ago by
Istvan Albert
100k
68
votes
25
replies
16k
views
12 follow
Tool:
sra-explorer : find SRA and FastQ download URLs in a couple of clicks
fastq
SRA
updated 6 months ago by
GenoMax
141k • written 5.2 years ago by
Phil Ewels
★ 1.4k
28
votes
4
replies
15k
views
Tool:
Plotting GSEA output in R
RNA-Seq
javaGSEA
GSEA
updated 10 months ago by
Ram
43k • written 7.7 years ago by
thomaskuilman
▴ 850
9
votes
13
replies
15k
views
Sort bam file by coordinates using samtools
next-gen-sequencing
gene
rna-seq
updated 10 months ago by
Ram
43k • written 5.6 years ago by
Shahzad
▴ 30
12
votes
10
replies
15k
views
6 follow
conversion of GFF3 formate to BED format
RNA-Seq
updated 11 weeks ago by
Ram
43k • written 5.9 years ago by
blooming.daisy333
▴ 110
15
votes
11
replies
15k
views
10 follow
TCGA/Broad Institute CNV Files Segment Mean
tcga
cnv
updated 5 months ago by
sativus
▴ 20 • written 9.6 years ago by
dirigible2012
▴ 320
31
votes
30
replies
15k
views
6 follow
Tool:
BioVinci: user-friendly software to make plotting easy - PCA, 3D scatter plot, venn diagram, you name it.
gene
RNA-Seq
Venn-diagram
PCA
updated 10 months ago by
Ram
43k • written 5.9 years ago by
Jennifer Pham
▴ 450
49
votes
18
replies
15k
views
12 follow
What Phylogeny Viewing Software Do You Use?
software
phylogenetics
visualization
updated 5 months ago by
Ram
43k • written 14.1 years ago by
Roderic Page
▴ 390
25
votes
7
replies
15k
views
Use samtools index on multiple bam files at the same time from the command line?
RNA-Seq
next-gen
sequence
updated 11 months ago by
Pierre Lindenbaum
161k • written 8.3 years ago by
nash.claire
▴ 490
1,000 results • Page
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Recent Votes
A: How to process (seems) Agilent microarrry data?
Comment: genome assembly records not present in assembly_summary.txt
Answer: genome assembly records not present in assembly_summary.txt
Answer: PCA plot (Suggestions Needed)
Comment: PCA plot (Suggestions Needed)
Comment: PCA plot (Suggestions Needed)
Comment: PCA plot (Suggestions Needed)
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Recent Replies
Comment: Low mapping rate with Salmon
by
i.sudbery
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…
Comment: How to convert plink files to Hapmap Format
by
bk11
★ 2.4k
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
GenoMax
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
by
pinheirofabiano
▴ 10
install.packages("pheatmap") library(pheatmap) setwd("/Users/data_analysis/results") data <- read.table(file…
Comment: Low mapping rate with Salmon
by
Patadu94
• 0
Thanks for the link GenoMax. But I was wondering, should not alignment and mapping have a similar rate and thus be correlated? In my case I…
Answer: Create a new bed file with all pairwise combinations between two other bed files
by
Pierre Lindenbaum
161k
bedtools intersect \ -a <(sort -t $'\t' -k1,1 -k2,2n A.bed) \ -b <(awk '{X=250000;P=int($2);printf("%s\t%d\…
Comment: Create a new bed file with all pairwise combinations between two other bed files
by
J
• 0
The command lines I wrote out for you are the ones I actually used. My original reference to bedtools intersect was because I assumed the b…
Comment: ScRNA data question
by
starswillfade
▴ 10
I just thought it was weird that considering each dot is a cell their expressions were all on a single line instead of being spread out lik…
Comment: ScRNA data question
by
starswillfade
▴ 10
![enter image description here][1] I am already using Seurat V5 I think. I am using SCTransform as it was recommended by the seurat page. I…
Answer: genome assembly records not present in assembly_summary.txt
by
GenoMax
141k
Can you clarify what `metainfo` you are referring to? The accession that you refer to does exist in [**GenBank assembly_summary file**][1…
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