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121,558 results • Page
1782 of 2432
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Votes
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0
votes
4
replies
2.5k
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datasets for brain cancer survival prediction
glioblastoma
clinical data
treatment patterns
8.9 years ago by
meeravarma.cev
▴ 20
3
votes
11
replies
7.8k
views
Calculating statistical significance of overlap between two groups of genes - adapting hypergeometric test for my situation?
r
genome
genes
overlap
significance
updated 8.9 years ago by
Nicolas Rosewick
11k • written 8.9 years ago by
Rubal
▴ 350
1
vote
2
replies
4.0k
views
MatrixeQTL FDR and Q-Qplot
MatrixeQTl
FDR
updated 2.1 years ago by
Ram
45k • written 10.3 years ago by
toyan.j.p
▴ 30
0
votes
0
replies
1.6k
views
Overall average coverage for different regions in 1000 Genomes
1000 genomes
coverage
8.9 years ago by
M. Möller
▴ 40
4
votes
9
replies
7.2k
views
How to handle the whole genome sequencing data using by plink?
plink
vcftools
WGS
sequencing
updated 8.9 years ago by
stu111538
▴ 80 • written 8.9 years ago by
line1438
▴ 40
4
votes
7
replies
2.2k
views
getting miRBase microRNAs gff Aspergillus fumigatus
RNA-Seq
miRNA
8.9 years ago by
zizigolu
★ 4.4k
0
votes
2
replies
2.5k
views
Looking for big data of SNPs in Alzheimer's disease
alzheimer
snp
big data
8.9 years ago by
Alexandra
• 0
0
votes
4
replies
2.0k
views
Intermediate range calculation from files
perl
python
updated 2.3 years ago by
Ram
45k • written 8.9 years ago by
User 6777
▴ 20
0
votes
2
replies
1.9k
views
Experience with SOAP trans
soap trans
de novo
updated 8.9 years ago by
Biostar
20 • written 8.9 years ago by
Biogeek
▴ 480
0
votes
1
reply
3.6k
views
Undefined reference ERROR in building the localized UCSC Genome browser with kent source
UCSC
local
make error
8.9 years ago by
2013302630028
▴ 10
0
votes
3
replies
3.8k
views
looking for TCGA gene expression Normal Samples
genome
sequence
updated 8.9 years ago by
nwon
▴ 60 • written 8.9 years ago by
Peter Chung
▴ 210
3
votes
5
replies
3.8k
views
annotating a vcf file containing Structural Variants
SNP
snp
gene
updated 8.9 years ago by
igor
13k • written 8.9 years ago by
Bogdan
★ 1.4k
1
vote
0
replies
2.7k
views
Can Read Back Phased genotypes be used to extend the haplotype blocks with Beagle, Shapeit, FastPhase etc?
Beagle
ShapeIt
FastPhase
ReadBackPhasing
Haplotype
8.9 years ago by
kirannbishwa01
★ 1.6k
0
votes
3
replies
7.1k
views
How to filter out duplicate records in a vcf with bcftools?
bcftools
vcf
updated 8.9 years ago by
Brice Sarver
★ 3.8k • written 8.9 years ago by
vitor.aguiar
▴ 10
1
vote
2
replies
2.4k
views
Counting ambiguously mapped reads per feature
RNA-Seq
gtf
bam
count
updated 8.9 years ago by
Biostar
20 • written 9.0 years ago by
rubic
▴ 270
0
votes
0
replies
1.7k
views
Conflicting differential expression results due to multiple matches in annotation
RNA-Seq
DESeq2
8.9 years ago by
NewtoRNAseq
• 0
0
votes
0
replies
1.6k
views
Can someone help me produce a circular genome figure from a genbank or fasta file?
genome
sequence
alignment
8.9 years ago by
jamesdemayo
• 0
10
votes
10
replies
3.9k
views
Statistics problem: Significance of BLAST e-values of two species
blast
gene
rbh
homolog
updated 8.9 years ago by
Andrzej Zielezinski
11k • written 8.9 years ago by
Gene Mustermann
▴ 10
2
votes
5
replies
2.1k
views
Parsing GLOBPROT flat text file format
python
updated 2.3 years ago by
Ram
45k • written 8.9 years ago by
User 6777
▴ 20
0
votes
1
reply
3.0k
views
Calculating FST from Transcriptomic Sequence Data stored in a VCF
RNA-Seq
FST
PopGenome
Sequence Data
de novo
8.9 years ago by
mek362
▴ 10
4
votes
8
replies
3.2k
views
Are there services/java libs I can use to upload files automatically for UCSC display?
java
ucsc
genome
browser
updated 8.9 years ago by
Ryan Dale
5.0k • written 8.9 years ago by
endrebak
▴ 980
0
votes
0
replies
3.4k
views
direct call of indels/snps with bcftools?
SNP
bcftools
updated 8.9 years ago by
Biostar
20 • written 8.9 years ago by
cristina_sabiers
▴ 110
2
votes
2
replies
2.3k
views
Find Mutations Frequencies by Cancer Type
sequencing
updated 8.9 years ago by
igor
13k • written 8.9 years ago by
L. A. Liggett
▴ 130
1
vote
1
reply
2.9k
views
What is the difference between RNA: Affy HG-U95(A-E), RNA: Affy HG-U133(A-B), RNA: Affy HG-U133 Plus 2.0 on the CellMiner
gene-expression
CellMiner
NCI60
updated 3.1 years ago by
Ram
45k • written 10.3 years ago by
zero_hsy
▴ 110
0
votes
1
reply
1.8k
views
Gene Regulatory Networks (GRN)
GRN
MATLAB
BAyesian
8.9 years ago by
Andrea
▴ 60
2
votes
1
reply
2.6k
views
Clinical significance ClinVar
clinvar
clinical significance
updated 8.9 years ago by
Denise CS
★ 5.2k • written 8.9 years ago by
onemoreuser
▴ 30
18
votes
19
replies
3.9k
views
Sorting sequences according header
software error
sequence
Assembly
next-gen
8.9 years ago by
Gian77
▴ 70
0
votes
4
replies
2.7k
views
rsubread exactsnp ERROR "memory not mapped"
Rsubread
exactSNP
updated 8.9 years ago by
GenoMax
152k • written 8.9 years ago by
tarek.mohamed
▴ 370
1
vote
1
reply
1.9k
views
How to analyze Cufflinks data
RNA-Seq
sequencing
updated 8.9 years ago by
Satyajeet Khare
★ 1.6k • written 8.9 years ago by
rydharri
• 0
24
votes
18
replies
9.3k
views
Should I remove Kmers identified in FastQC?
next-gen
genome
FastQC
updated 2.5 years ago by
Ram
45k • written 10.1 years ago by
kezcleal
▴ 160
0
votes
1
reply
1.9k
views
Unexpected sample clustering after microarray normalization
microarray
normalization
PCA
clustering
8.9 years ago by
lvaremo
• 0
1
vote
6
replies
2.8k
views
General phylogenetic tree package
python
r
phylogenetic
tree
updated 8.9 years ago by
Jean-Karim Heriche
27k • written 8.9 years ago by
shai2go
• 0
1
vote
2
replies
5.3k
views
How to Calculate the genetic distance between SNPs with the positions known
SNP
updated 2.7 years ago by
Ram
45k • written 10.0 years ago by
ice4prince
▴ 10
1
vote
1
reply
1.9k
views
RSVSim cannot simulate duplications
simulation
software error
genome
updated 8.9 years ago by
choosehappy
▴ 10 • written 9.0 years ago by
bdelolmo
▴ 10
2
votes
2
replies
6.0k
views
How to get different colors on coverage tracks in IGV
IGV
RNA-Seq
updated 8.9 years ago by
Carlo Yague
9.0k • written 8.9 years ago by
jon.brate
▴ 310
3
votes
3
replies
2.7k
views
Retrieve tissue expression in Zfin (R/python)
Danio-rerio
Zfin
zebrafish
updated 3.0 years ago by
Ram
45k • written 9.5 years ago by
A. Domingues
★ 2.7k
3
votes
4
replies
1.9k
views
Extracting information from a large fasta header formatted file
perl
python
updated 2.3 years ago by
Ram
45k • written 8.9 years ago by
User 6777
▴ 20
21
votes
24
replies
4.3k
views
Forum:
From DEGs of a non-model animals to statistically significantly enriched pathways
pathway-enrichment
GO
RNA-Seq
KEGG
updated 2.3 years ago by
Ram
45k • written 8.9 years ago by
Farbod
★ 3.4k
9
votes
8
replies
16k
views
t-test or linear regression?
R
updated 8.9 years ago by
russhh
5.8k • written 8.9 years ago by
moxu
▴ 510
2
votes
4
replies
2.2k
views
Pooling microarray data
microarray
pool
updated 8.9 years ago by
Jean-Karim Heriche
27k • written 8.9 years ago by
grayapply2009
▴ 300
0
votes
0
replies
1.3k
views
How to interpret the Phase plot of jarnac (Systems biology workbench)
software
8.9 years ago by
glady
▴ 320
4
votes
7
replies
2.8k
views
repeated read ids from Illumina MiniSeq fastq.gz files?
fastq
illumina
updated 2.3 years ago by
Ram
45k • written 8.9 years ago by
14134125465346445
★ 3.6k
3
votes
1
reply
2.7k
views
KEGG graph or pathway to Adjacency matrix
kegg
adjacency matrix
R
updated 8.9 years ago by
Jean-Karim Heriche
27k • written 8.9 years ago by
saamar.rajput
▴ 80
0
votes
1
reply
1.4k
views
Paternity index with snp mutation
SNP
PI
forensics
mutation
8.9 years ago by
promer
• 0
5
votes
6
replies
2.3k
views
How to sequence a gene along with its 3' and 5' UTR
gene
sequence
UTRs
updated 8.9 years ago by
Carlo Yague
9.0k • written 8.9 years ago by
Shahzad
▴ 30
11
votes
13
replies
4.1k
views
News:
Ensembl datacentre shut-down: Friday 26th August - Tuesday 30th August 2016
Maintenance
Ensembl
updated 2.3 years ago by
Ram
45k • written 8.9 years ago by
Ben Moore
★ 2.4k
36
votes
9
replies
25k
views
merging two bigwig files
ChIP-Seq
deeptools
bigwig
merge
updated 8.9 years ago by
Devon Ryan
105k • written 8.9 years ago by
ATCG
▴ 400
0
votes
1
reply
2.8k
views
N50 Of Meta-Velvet Output
updated 8.9 years ago by
Biostar
20 • written 12.1 years ago by
deepthithomaskannan
▴ 420
3
votes
5
replies
3.3k
views
Determining Paired-end or Mate-pair insert length in De Novo Sequencing
De novo
paired end
mate pair
updated 8.9 years ago by
Charles Plessy
★ 2.9k • written 8.9 years ago by
sameedmsiddiqui
▴ 20
0
votes
1
reply
1.8k
views
how to extract all reads covered at the somatic SNP site that from a BAM file in VCF file with using python?
alignment
next-gen
SNP
sequencing
8.9 years ago by
winter_li
▴ 60
121,558 results • Page
1782 of 2432
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Answer: RNA-Seq paired-end datasets
Comment: why bwa-mem only return one read with pair-read end
A: Length of the amplicon after trimming
A: Length of the amplicon after trimming
Answer: Extract UMIs using UMI-tools
Comment: Understanding NCBI vs ENA data
Answer: Best strategy for comparing cell-type composition between disease and healthy gr
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Answer: RNA-Seq paired-end datasets
by
Matthias Zepper
5.1k
There are many. Just go to [GEO Data Sets][1] and enter something like `("rats"[MeSH Terms] OR "Rattus norvegicus"[Organism]) AND ("gse"[Fi…
Comment: Identification problem of IDE-8 cell on culture with inverted microscope
by
i.sudbery
21k
This post does not fit the theme of this forum.
Comment: Understanding NCBI vs ENA data
by
i.sudbery
21k
Both places should have checksums available - you could look if they were the same.
Comment: RNA-seq assigned alignments
by
jaro.slamecka
▴ 270
To reiterate one of GenoMax's questions, is the new sequencing provider making the libraries for you? If so, have they by any chance used r…
Answer: Best strategy for comparing cell-type composition between disease and healthy gr
by
jared.andrews07
★ 19k
I'd recommend reading the [differential abundance testing chapter](https://bioconductor.org/books/3.21/OSCA.multisample/differential-abunda…
Comment: How do you clean GEO metadata before downstream analysis?
by
yura.grabovska
▴ 800
They did make a [Tool post originally](https://www.biostars.org/p/9613596), but still phrased it as something they just came across rather …
Comment: How do you clean GEO metadata before downstream analysis?
by
jared.andrews07
★ 19k
Agreed, just make a "Tool" post if you want to spread the word about it. People tend to take those much better than these weak attempts at…
Comment: RNA-seq assigned alignments
by
GenoMax
152k
Since you have decided to move to a new sequence provider that decision is for economic reasons and not scientific, so not much to think ab…
Comment: Obtain Common SNPS for Mouse Genome
by
GenoMax
152k
These are multi-strain VCF's so you could look for SNP's common across the strains (see --> https://www.biostars.org/p/9498113/ ) . Keep in…
Comment: RNA-seq assigned alignments
by
Manko47
▴ 10
>Are you comparing the same exact library sequenced by two different companies. Nah it's just majorty of my old datasets osciliated around…
Answer: RNA-seq assigned alignments
by
GenoMax
152k
> Previously on the single-end data from old company I was getting around 50-60% of the uniquely aligned reads Are you comparing the same…
Comment: Extract track data from "search by region" feature on ENCODE
by
AlienPumpkinPie
• 0
Thank you for your reply! Yeah I thought the same. It feels weird to me that this is not an obvious feature.
Comment: How do you clean GEO metadata before downstream analysis?
by
yura.grabovska
▴ 800
Again... "I recently *stumbled* upon a small browser-based tool" On the site: "Created by alba0gf" That's the second time you've linked y…
Comment: Tool to clean GEO metadata
by
yura.grabovska
▴ 800
"i recently *found* this simple tool" Go to site "Created by alba0gf" I mean... why lie?
Comment: DGE analysis in Seurat using paired samples per donor ?
by
yura.grabovska
▴ 800
What do you think you'll gain by doing tumour vs normal at single-cell resolution? The whole point of single cell is to define sub-populati…
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