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999 results • Page
4 of 20
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0
votes
1
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190
views
Alternatives to metanalyisis. P integration. Horiztonal integration RNA-seq
rna-seq
updated 6 days ago by
i.sudbery
19k • written 7 days ago by
Edmond
• 0
0
votes
0
replies
147
views
What open-source tools can determine the coverage/completion of a pathway based on EC numbers?
metagenomics
metacyc
enzyme
pathway
genomics
7 days ago by
O.rka
▴ 710
0
votes
1
reply
685
views
after selecting specific GO terms to plot, cneplot is not showing any color for genes, GO terms and only showing lines without nodes.
cneplot
updated 7 days ago by
Ram
43k • written 7 days ago by
Dr Huma Naz
• 0
2
votes
2
replies
282
views
p-value in CIBERSORT
CIBERSORT
p-value
7 days ago by
michelafrancesconi9
▴ 20
0
votes
5
replies
382
views
Telescope issue
Telescope
RNA-seq
updated 6 days ago by
GenoMax
142k • written 7 days ago by
eleven11
• 0
5
votes
6
replies
535
views
Programmatically retrieving positions of protein active site residues
Uniprot
PDB
Proteins
updated 7 days ago by
me
▴ 760 • written 8 days ago by
Mariana
▴ 40
1
vote
1
reply
238
views
Adjust pvalue in R with different approach give me all different outcome
statistics
R
p-value
updated 7 days ago by
Ram
43k • written 7 days ago by
Jonathan Yoou
▴ 60
1
vote
2
replies
296
views
Minimum RAM and Storage requirement for creating PSSM using ncbi-blast-2.2.30+-x64-linux
blast
pssm
6 days ago by
Nafi
• 0
1
vote
3
replies
288
views
What does 'bundle_uuid' refer to in this metadata sheet?
SRA
illumina
GEO
metadata
updated 7 days ago by
GenoMax
142k • written 7 days ago by
jeffrey.maurer.informatics
• 0
1
vote
3
replies
284
views
ERROR When Using Ensembl Plants Biomart Wget API
biomart
plant
ensembl
2 days ago by
Dora
▴ 10
0
votes
0
replies
169
views
News:
Goodbye, Slow Code? How BioNumpy can Redefine Python’s Role in Bioinformatics!
BioNumPy
Python
NumPy
updated 7 days ago by
Ram
43k • written 7 days ago by
Chakri
• 0
0
votes
2
replies
228
views
RNA editing sites based on DNA seq and RNA seq
RNA-editing
20 hours ago by
Ahiad Chen Zion
• 0
1
vote
5
replies
334
views
Introduce SNPs on FASTA
simulation
snps
haplotypes
pharmacogenetics
5 days ago by
Riccardo
▴ 10
0
votes
0
replies
134
views
News:
Online course: Meta-analysis in R - last 2 seats left
Meta-Analysis
Statistics
R
updated 7 days ago by
Ram
43k • written 7 days ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
128
views
Somatic variant calling with Mutect2 using 2 matched-normals for one sample
cancer
mutect
variant-calling
GATK
somatic-variants
updated 7 days ago by
Ram
43k • written 7 days ago by
Alexandros
• 0
0
votes
1
reply
176
views
unable to get feature count results
featureCounts
updated 7 days ago by
Ram
43k • written 7 days ago by
Ravita
• 0
0
votes
3
replies
292
views
KEGG Pathways
r
RNA-seq
updated 7 days ago by
Ram
43k • written 7 days ago by
Sudip
• 0
4
votes
6
replies
3.9k
views
Taking the difference of two VCFs (or removing singletons)
genome
sequencing
singleton
SNP
filter
updated 7 days ago by
Andres
▴ 20 • written 9.6 years ago by
hermathena
▴ 40
0
votes
0
replies
135
views
Seurat object reductions (PCA, UMAP,..) after subsetting data
Seurat
7 days ago by
Bine
▴ 60
0
votes
1
reply
292
views
News:
FINAL CALL: 8th Berlin Summer School in NGS Data Analysis - Only a few last places available
DNA-seq
variant-calling
RNA-seq
illumina
transcriptomics
8 days ago by
David Langenberger
11k
0
votes
1
reply
192
views
Deseq2
Deseq2
updated 8 days ago by
Jack Tierney
▴ 360 • written 8 days ago by
Sudip
• 0
1
vote
1
reply
239
views
Polishing genome assembly
polishing
Nanopore
PacBio
updated 8 days ago by
Michael
54k • written 8 days ago by
Lissa Cruz Saavedra
• 0
5
votes
3
replies
288
views
6 follow
Integrate transcriptomic data and proteomics data.
OMICS
updated 8 days ago by
Lluís R.
★ 1.2k • written 8 days ago by
이민경[학생](대학원 융합의과학과)
• 0
2
votes
2
replies
204
views
MA plot of shrunken fold change
MA-plot
Deseq2
updated 8 days ago by
ATpoint
82k • written 8 days ago by
Sudip
• 0
1
vote
2
replies
229
views
Need help for downloading arabdopsis thaliana reference genome fasta file and gtf file
Arabidopsis-thaliana
gtf
reference-genome
updated 7 days ago by
Ram
43k • written 8 days ago by
Ravita
• 0
3
votes
3
replies
224
views
Gene Specific coverage from WGS data
linux
WGS
Bioinformatics
SARS
CoV2
1 day ago by
Adyasha
• 0
0
votes
0
replies
116
views
human gut metagenome taxonomy profile table and KO profile table from big cohort
metagenome
gut
human
8 days ago by
fanglujing
▴ 60
0
votes
0
replies
134
views
Are some metagenomes too complex for MAGs?
metagenomics
metagenome
MAGs
assembly
8 days ago by
Jacob
• 0
0
votes
3
replies
748
views
Why cd-hit-est not work when sequence identity threshold<0.95?
genome
cluster
sequence
updated 8 days ago by
weidonglu
• 0 • written 21 months ago by
JZX
• 0
0
votes
4
replies
283
views
Perfom a Gene Ontology Analysis from GO terms txt file
RNA-Seq
GO
updated 8 days ago by
Ram
43k • written 8 days ago by
Hamtaro
▴ 50
0
votes
1
reply
185
views
Differential Accessibility
DiffBind
updated 8 days ago by
Ram
43k • written 8 days ago by
Shloka
• 0
0
votes
3
replies
297
views
Landmark gene selection in L1000.
L1000
landmark-gene
cmap
updated 7 days ago by
GenoMax
142k • written 8 days ago by
kim
• 0
3
votes
2
replies
390
views
Extract protein sequence
fasta
alignment
blast
7 days ago by
anna
▴ 20
3
votes
3
replies
325
views
Is it possible to bulk download files from GEO repository?
RNA-seq
Galaxy
Tanscriptomics
updated 8 days ago by
noodle
▴ 580 • written 9 days ago by
WUSCHEL
▴ 750
0
votes
1
reply
170
views
metagenomic virome quality assessment
viromics
metagenomics
updated 8 days ago by
Ram
43k • written 8 days ago by
Petchimuthu
• 0
3
votes
7
replies
351
views
FastQC Quality per tile and per sequence behaving strange after using Cutadapt
fastqc
cutadapt
illumina
tile
paired-end
8 days ago by
salias
• 0
0
votes
0
replies
128
views
Using limma in methylation EM-seq?
EM-seq
methylation
8 days ago by
Lluís R.
★ 1.2k
4
votes
7
replies
594
views
Very low RNA splicing rate for pulmonary AT2 cells
RNA-velocity
scVelo
scRNA-seq
splicing
8 days ago by
e.r.zakiev
▴ 210
0
votes
0
replies
125
views
Synteny analysis
bacterial
synteny
genome
updated 8 days ago by
GenoMax
142k • written 8 days ago by
Namil
• 0
0
votes
4
replies
267
views
Genbank File Format
gbkformat
8 days ago by
alenew.am
• 0
0
votes
5
replies
434
views
How should I make kallisto indexes?
kallisto
updated 8 days ago by
dsull
★ 6.0k • written 22 days ago by
bioinfo
▴ 150
0
votes
0
replies
242
views
Assist me in determining whether the analysis process using the limma package has been executed correctly
limma
ArrayExpress
DifferentialExpression
GEOquery
8 days ago by
SSSJec
• 0
0
votes
3
replies
222
views
Software to separate reads from different individuals
software
development
nanopore
updated 8 days ago by
GenoMax
142k • written 8 days ago by
njornet
▴ 20
0
votes
2
replies
257
views
How to update R on ubuntu
installation
update
R
apt-get
8 days ago by
Bosberg
▴ 50
4
votes
0
replies
140
views
Herald:
The Biostar Herald for Monday, April 29, 2024
herald
8 days ago by
Biostar
2.7k
1
vote
1
reply
147
views
Two references 1. genome 2. plasmid for bowtie2
WGS
BacterialGenomics
Alignment
updated 8 days ago by
GenoMax
142k • written 9 days ago by
Ruqaiya
• 0
0
votes
1
reply
277
views
Using Delly/Pindel/breakdancer for Identifying Transgene Insertion Sites in Mouse Genome
breakdancer
insertion
Pindel
variation
Delly
updated 8 days ago by
trausch
★ 1.9k • written 25 days ago by
zec018
• 0
0
votes
0
replies
111
views
LEfSe
LEfSe
8 days ago by
benkosta
• 0
0
votes
0
replies
93
views
How should I handle read counts derived from SGSeq when I want to build DEXSeqDataSet object
DEXSeq
DEXSeqDataSet
SGSeq
8 days ago by
Sara
▴ 30
1
vote
4
replies
409
views
Limma Analysis Agilent Microarray Data (GPL1708)
Microarray
Limma
Agilent
8 days ago by
hagl
▴ 10
999 results • Page
4 of 20
Recent Votes
Answer: TFs and Gene databases
Answer: TFs and Gene databases
Answer: TFs and Gene databases
Comment: java out of memory error through beagle for imutation
Analysis of intronic reads included scRNA-seq data
removeBatchEffect explained using base R linear models
Answer: ChIP-seq datasets: input samples omitted?
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sooni
▴ 20
Teacher
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jared.andrews07
★ 16k
Popular Question
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synat.keam
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Recent Replies
Comment: TFs and Gene databases
by
ijarne
• 0
Thank you so much @jaredandrews07 it looks like I will be able to get what I intended with these sources !!
Comment: Percentage coverage of reference genome by de novo genome
by
Joe
21k
If you have contigs for assemblies, using read-based approaches like samtools is probably not the way to go. As you're interested in % cov…
Comment: Exploring Diet Effects in Single-Cell RNA Sequencing
by
ATpoint
82k
Has data been generated in the same batch, so same day, in the same 10x runs?
Answer: Comparative Analysis of Algorithms for Implementing the FM-Index: Correctness, C
by
Michael
54k
So I am assuming you have calculated a Burrows-Wheeler transform, then add the FM-index for the first and last column of the BW-matrix. I r…
Comment: STAR aligner error
by
M.
▴ 30
I already told them but they couldn't come up with a useful solution :/
Comment: A question about reference genome for creating the consensus sequence
by
ATpoint
82k
You aligned your data, that is your reference genome to compare against. If you want to change reference then realign.
Comment: Applying the metacell2 algorithm using python
by
JACKY
▴ 140
The vignette I followed, although lacking, seems better since it focuses on doing iterative process. I'll keep looking perhaps I'll find so…
Comment: A question about reference genome for creating the consensus sequence
by
me
• 0
Hi, yes, my cram files cover the whole genome, which is actually individual genome information. I wonder how to adjust the base genome. Tha…
Comment: CNVKIT - unable to produce scatter and diagram pdfs
by
DGTool
• 0
At least according to the documentation, it seems for WGS you can use the `batch --method wgs` option. There is more information here: [htt…
Answer: A question about reference genome for creating the consensus sequence
by
ATpoint
82k
It is the consensus for all reads that overlap a given base, it's not a genome consensus unless your reads cover the entire genome.
Answer: CNVKIT - unable to produce scatter and diagram pdfs
by
Anitha
• 0
Hello everyone, I need to call the CNV from my hunam WGS data. I searched for many tutorial, but I did'nt get any proper procedure. I am tr…
Comment: High Malat-1 expression in single cell data
by
t.montserrat.ayuso
▴ 30
I don't think dropout is playing an important role with Malat1 since it is usually highly expressed. On the other hand, if dropout is still…
Comment: java out of memory error through beagle for imutation
by
analyst
▴ 40
Resolved by increasing heapsize of -Xmx50G
Comment: STAR aligner error
by
Ram
43k
Talk to your HPC sysadmin - array jobs might be getting different kinds of nodes compared to standalone jobs.
Comment: Is therer any suggestions on mapping rate of WGBS data?
by
Zeng Jingyu
▴ 60
Thank you for your answer!
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