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77 results • Page
2 of 2
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Views
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0
votes
1
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130
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
0
replies
130
views
RNA-seq: full length gene
RNA-seq
updated 2 days ago by
Ram
43k • written 2 days ago by
Nargis
• 0
1
vote
0
replies
123
views
Simulation of label-free bottom-up proteomics expression dataset
label-free
bottom-up
lc-ms
proteomics
2 days ago by
KABILAN
▴ 50
0
votes
0
replies
122
views
Haplotype Phased Assembly Contigs to Chromosome Annotations
Assembly
phased
Haplotype
Annotation
2 days ago by
turcoa1
• 0
0
votes
0
replies
118
views
Alternative splicing analysis using SUPPA tool - how to normalise counts?
rna-seq
single-cell
suppa
alternative-splicing
updated 3 days ago by
Ram
43k • written 4 days ago by
newuser2024
• 0
0
votes
0
replies
110
views
Pairwise alignment and Ka/Ks computation
Pairwise-Alignment
Genomics
Ka-Ks
updated 5 days ago by
Ram
43k • written 5 days ago by
maxime.policarpo
▴ 200
0
votes
0
replies
107
views
AttributeError: module 'scvelo' has no attribute 'pp
loomfile
scvelo
scipy
annData
numpy
4 days ago by
Kash
▴ 110
0
votes
0
replies
101
views
Is result interpretation of the modelHomotypic function of the DoubletFinder correct?
doublet
DoubletFinder
Seurat
modelHomotypic
updated 3 days ago by
Ram
43k • written 4 days ago by
Jeyong
• 0
0
votes
0
replies
98
views
Merging replicates from Encode project
CHIP-seq
encode
5 days ago by
Nurken
• 0
0
votes
0
replies
98
views
The concept of co-occurrence network structure
co-occurence
microbiome
network
5 days ago by
ohtang7
▴ 40
0
votes
0
replies
97
views
File with NCBI summary or Uniprot description
annotation
visualisation
NCBI
Uniprot
RNA
updated 5 days ago by
Ram
43k • written 5 days ago by
Amélie
• 0
0
votes
0
replies
93
views
Analysis of the gene family of a genome.
Genome
gene-family
updated 5 days ago by
Ram
43k • written 5 days ago by
sansan_96
▴ 80
0
votes
0
replies
92
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
92
views
Trimming best practices for SNP calling
trimming
SNP
trimmomatic
6 days ago by
Enrique
• 0
0
votes
0
replies
88
views
Help with finding conferences in immuno-informatics/virology
virology
conferences
immunology
6 days ago by
manaswwm
▴ 510
0
votes
0
replies
87
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 5 days ago by
SSSJec
• 0
0
votes
0
replies
86
views
How to get somatic variation based on RNA-seq data?
RNA-seq
variation
somatic
6 days ago by
feather-W
• 0
0
votes
0
replies
85
views
Annotating single cell data automatically
cell
annotation
single
6 days ago by
Gerard
• 0
0
votes
0
replies
82
views
Difficulties getting **the adjacency file** necessary for **aracne2regulon** function.
VIPER
MARINA
ARACNe
6 days ago by
Biostars2200
• 0
0
votes
0
replies
82
views
Extract protein sequence
fasta
alighment
blast
20 hours ago by
anna
▴ 20
0
votes
0
replies
80
views
Filtering most similarly expressed gene (contrary to differential expression gene) with NOISeq?
NOIseq
5 days ago by
alifafiq1
• 0
0
votes
0
replies
80
views
Filter low express genes in microarray data
microarray
21 hours ago by
Chris
▴ 260
0
votes
0
replies
77
views
STAR total splices (in Log.final) vs collapsed splice junctions (in SJ.out.tab)
STAR
19 hours ago by
tnminh89
▴ 10
0
votes
0
replies
75
views
Correct way of reducing predictive model complexity
lasso
glmnet
predictvemodeling
regression
6 days ago by
sativus
▴ 20
0
votes
0
replies
74
views
Imputation advice
imputation
6 days ago by
kl
▴ 10
0
votes
1
reply
53
views
Downloading full alignments from Pfam
pfam
updated 1 hour ago by
GenoMax
141k • written 5 hours ago by
bef1
• 0
0
votes
0
replies
48
views
adjusting for confounders in LMER in R
confounders
LMER
R
9 hours ago by
rene.j.erhardt
▴ 20
77 results • Page
2 of 2
Recent Votes
How to input margin to UpsetR figure
Comment: How to assign cell types after integration in scRNA
NGS forensics: how to know if data is fabricated
Answer: ChIP-seq datasets: input samples omitted?
Comment: Help understanding how KEGG Ortholog `K00004 ` has 3 ECs associated with it (EC:
A: Deeptools plotHeatmap - Maintain Order of Input BED file
Comment: NGS forensics: how to know if data is fabricated
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Recent Replies
Comment: Downloading full alignments from Pfam
by
GenoMax
141k
Not as convenient but the entire set of full alignments can be downloaded here: https://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pf…
Comment: How many reads for WGS Sequencing?
by
GenoMax
141k
> What does clipped Fastq mean? Probably means that NCBI has already scanned and trimmed adapter sequencers. > both forward and revers…
Comment: How many reads for WGS Sequencing?
by
GenoMax
141k
You can use the default `adapters.fa` file included in the `resources` folder of [**BBMap suite**][1] (program to use is `bbduk.sh`) or a p…
Comment: How many reads for WGS Sequencing?
by
GenoMax
141k
Only way to find out is to try. It may work but if it is not going to then you will find that out quick (process would likely crash because…
Comment: How many reads for WGS Sequencing?
by
Ruqaiya
• 0
Also, there is no mention of adapter sequence so which adapter sequence should i use to remove it from some other reads?
Comment: How many reads for WGS Sequencing?
by
Ruqaiya
• 0
Also, Do you think i can reproduce at least most part of the data from the paper just on my laptop? It has 4 logical processors (Intel(R) C…
Comment: NGS forensics: how to know if data is fabricated
by
Philipp Bayer
8.3k
While I think this is an interesting case, I've before found cleaned 'raw' data on SRA. It happens: bioinformaticians receive the raw data,…
Comment: How many reads for WGS Sequencing?
by
Ruqaiya
• 0
1. What does clipped Fastq mean? both forward and reverse reads in the same file? 2. Why would you remove 2000bp contigs? I feel it will gi…
Comment: How many reads for WGS Sequencing?
by
Ruqaiya
• 0
Well, I downloaded both the reads from-[LINK][1]. Thats all i did. Thats the only thing i need to do, right? I'l try spades. [1]: http…
Comment: How to assign cell types after integration in scRNA
by
Francesco
▴ 10
Thanks for the fast reply.. however i had only partially understood the answer. Is correct saying that low-representation integration and b…
Answer: Can I run cellassign on samples independently if there is batch effect present?
by
Francesco
▴ 10
Hi! Whenever you do make independent analysis or aggregate data and analyze them, most cell type assignment tools start from raw counts to …
Comment: gvcf joint calling
by
zihanss
• 0
Thanks for your comment, I get it now.
Answer: ChIP-seq datasets: input samples omitted?
by
ATpoint
82k
In my hands (and from what I know based on many years here) inputs are almost exclusively used during peak calling to correct for loci-spec…
Comment: How to assign cell types after integration in scRNA
by
ATpoint
82k
No difference here. After all you typically want a label per cluster/group, so either subset to the control condition to do the assignment,…
Comment: Differential Expression using Isoseq-supplemented reference transcriptome
by
gaoanwei
• 0
I found the question and ASK the GPT4 turbo
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