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79 results • Page
2 of 2
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Views
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0
votes
1
reply
139
views
tbtool
tbtool
updated 6 days ago by
Ram
43k • written 6 days ago by
Raman
• 0
0
votes
0
replies
138
views
One error problem occurred caused by data type during using GDCprepare to handle BRCA data
TCGA
GDCprepare
updated 4 days ago by
Ram
43k • written 4 days ago by
glaciya2018
• 0
0
votes
1
reply
132
views
Displaced fragment length distribution in ATAC-seq
ATAC-seq
nucleosome
fragment
updated 6 days ago by
ATpoint
82k • written 6 days ago by
enanoide
• 0
0
votes
1
reply
125
views
Finding batch and outlayers
Pca
updated 3 hours ago by
christopher medway
▴ 450 • written 12 hours ago by
Tigran
• 0
0
votes
0
replies
120
views
Extract protein sequence
fasta
alighment
blast
1 day ago by
anna
▴ 20
0
votes
0
replies
119
views
Alternative splicing analysis using SUPPA tool - how to normalise counts?
rna-seq
single-cell
suppa
alternative-splicing
updated 4 days ago by
Ram
43k • written 5 days ago by
newuser2024
• 0
0
votes
1
reply
117
views
Downloading full alignments from Pfam
pfam
updated 20 hours ago by
GenoMax
141k • written 1 day ago by
bef1
• 0
0
votes
0
replies
111
views
Filter low express genes in microarray data
microarray
1 day ago by
Chris
▴ 260
0
votes
0
replies
110
views
AttributeError: module 'scvelo' has no attribute 'pp
loomfile
scvelo
scipy
annData
numpy
5 days ago by
Kash
▴ 110
0
votes
0
replies
110
views
Pairwise alignment and Ka/Ks computation
Pairwise-Alignment
Genomics
Ka-Ks
updated 6 days ago by
Ram
43k • written 6 days ago by
maxime.policarpo
▴ 200
0
votes
0
replies
105
views
STAR total splices (in Log.final) vs collapsed splice junctions (in SJ.out.tab)
STAR
1 day ago by
tnminh89
▴ 10
0
votes
0
replies
102
views
Is result interpretation of the modelHomotypic function of the DoubletFinder correct?
doublet
DoubletFinder
Seurat
modelHomotypic
updated 4 days ago by
Ram
43k • written 5 days ago by
Jeyong
• 0
0
votes
0
replies
100
views
Merging replicates from Encode project
CHIP-seq
encode
6 days ago by
Nurken
• 0
0
votes
0
replies
99
views
The concept of co-occurrence network structure
co-occurence
microbiome
network
5 days ago by
ohtang7
▴ 40
0
votes
0
replies
98
views
File with NCBI summary or Uniprot description
annotation
visualisation
NCBI
Uniprot
RNA
updated 5 days ago by
Ram
43k • written 6 days ago by
Amélie
• 0
0
votes
0
replies
93
views
Analysis of the gene family of a genome.
Genome
gene-family
updated 6 days ago by
Ram
43k • written 6 days ago by
sansan_96
▴ 80
0
votes
0
replies
93
views
Software to calculate RSCU, ENC other than codonw
rscu
codonw
updated 5 days ago by
Ram
43k • written 5 days ago by
SHREYA
• 0
0
votes
0
replies
89
views
Help with finding conferences in immuno-informatics/virology
virology
conferences
immunology
6 days ago by
manaswwm
▴ 510
0
votes
0
replies
88
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
HMMcopy
Copy-number-analysis
R
updated 5 days ago by
Ram
43k • written 6 days ago by
SSSJec
• 0
0
votes
0
replies
81
views
adjusting for confounders in LMER in R
confounders
LMER
R
1 day ago by
rene.j.erhardt
▴ 20
0
votes
0
replies
80
views
Filtering most similarly expressed gene (contrary to differential expression gene) with NOISeq?
NOIseq
6 days ago by
alifafiq1
• 0
0
votes
2
replies
47
views
Longitudinal analysis of subpopulations: which approach is better?
differential-expression
DEG
model
1 hour ago by
Lluís R.
★ 1.2k
0
votes
1
reply
44
views
What should I consider as FASTA for dataset?
PDB
FASTA
updated just now by
GenoMax
141k • written 5 hours ago by
Nafi
• 0
0
votes
0
replies
41
views
vg call vs vg surject
vg
variation
graphs
updated just now by
GenoMax
141k • written 7 hours ago by
aliraza3119
• 0
0
votes
1
reply
40
views
Can I merge Hi-C fastq files from different lanes?
GenomeAssembly
BWA-MEM2
Hi-C
updated just now by
GenoMax
141k • written 7 hours ago by
Winter
• 0
0
votes
0
replies
35
views
Comparing peptide sequences with MS/MS peptide data using MaxQuant
Transcriptomics
Mass
Bioinformatics
spectrometry
Proteins
4 hours ago by
atharvakarkare14
▴ 10
0
votes
0
replies
35
views
Differential accessibility using DiffBinf
diffbind
6 hours ago by
Shloka
• 0
0
votes
0
replies
11
views
LEfSe
LEfSe
26 minutes ago by
benkosta
• 0
0
votes
0
replies
9
views
How should I handle read counts derived from SGSeq when I want to build DEXSeqDataSet object
DEXSeq
DEXSeqDataSet
SGSeq
47 minutes ago by
Sara
▴ 30
79 results • Page
2 of 2
Recent Votes
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A: vcf calculation of allele counts and allele number
Answer: Limma Analysis Agilent Microarray Data (GPL1708)
which tool/software/package should I use to preprocess the rosetta-merck microarray platform raw data?
Answer: How many reads for WGS Sequencing?
Comment: NGS forensics: how to know if data is fabricated
Comment: NGS forensics: how to know if data is fabricated
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Recent Replies
Comment: What should I consider as FASTA for dataset?
by
GenoMax
141k
> Should I use the shortened FASTA from pdb or should I use the full FASTA for my dataset? What analysis are you trying to use the data fo…
Comment: Is it possible to bulk download files from GEO repository?
by
GenoMax
141k
Galaxy specific requests are best posted on their help forum: https://help.galaxyproject.org/
Answer: Two references 1. genome 2. plasmid for bowtie2
by
GenoMax
141k
You can simply `cat` all reference sequences together. Create an index file with `bowtie2` and then align as usual.
Answer: High Malat-1 expression in single cell data
by
ATpoint
82k
My comment is general since I've never looked at this gene specifically, but metrics of poor cell quality in my experience never come alone…
Comment: What does it mean single base resolution in sequencing?
by
GenoMax
141k
>You known, 90% + genomic region is transcripted. So, total RNA-seq theoretically covers most genome region. Perhaps but not all of that …
Answer: Using Delly/Pindel/breakdancer for Identifying Transgene Insertion Sites in Mous
by
trausch
★ 1.9k
For [delly][1], we usually augment the mouse reference genome with the additional sequence, then remap and then look in the delly output fo…
Comment: NGS forensics: how to know if data is fabricated
by
i.sudbery
19k
Thats very intersting! What are the features in your classifier?
Answer: Limma Analysis Agilent Microarray Data (GPL1708)
by
hagl
▴ 10
Thank you very much for the response. Following your recommendation in pursuing option one by selecting highest expressions and subsequent …
Answer: RNAseq one control two conditions, shared and exclusive genes
by
Mohamed Abderrahmane
▴ 20
I think it would be pertinent to use DESEq2 to perform two comparisons: the first one between the control group and condition 1, and the se…
Comment: Longitudinal analysis of subpopulations: which approach is better?
by
Lluís R.
★ 1.2k
Many thanks for the helpful comment. Indeed, I read some of them, but I was not fully convinced and I missed the link FAQ of DESeq2. The re…
Comment: Longitudinal analysis of subpopulations: which approach is better?
by
ATpoint
82k
Keeping data together is most powerful and most convenient as you have a single analysis object and a single count matrix. I would always d…
Comment: Questions about a bug when transferring cram file to bam file
by
jkbonfield
★ 1.2k
Assuming you have network access and the md5sum is registered with the EBI's reference server, yes - it'll be downloaded and cached locally.
Comment: Downsampling fastq file
by
marco.barr
▴ 80
I followed your advice and it seems that I'm getting results comparable to what I was getting before. Upon checking with `wc -l` on the ori…
Comment: Finding batch and outlayers
by
christopher medway
▴ 450
You could perform an ANOVA to test if there is a significant association between batch number and a given Principal Component
Comment: ChIP-seq datasets: input samples omitted?
by
i.sudbery
19k
Fascinating! We also use inputs when doing metagene to protect against those situations where regions up or downstream of our metagene al…
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