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29 results • Page
1 of 1
Sort: Views
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Views
Votes
Replies
64
votes
25
replies
57k
views
22 follow
Download All The Bacterial Genomes From Ncbi
ncbi
updated 2 hours ago by
GenoMax
142k • written 11.4 years ago by
rehma.ar
▴ 290
4
votes
6
replies
12k
views
Looking for differential gene expression between treatment, within a specific cluster (seurat)
seurat
updated 19 hours ago by
jared.andrews07
★ 17k • written 4.7 years ago by
cook.675
▴ 230
3
votes
9
replies
5.2k
views
txt file to bigwig
MEME
bigwig
updated 58 minutes ago by
sogand
• 0 • written 8.5 years ago by
tanni93
▴ 50
8
votes
7
replies
3.9k
views
6 follow
What is the best practice of scRNA workflow for multiple patients and samples using Seurat
scRNA
sing-cell RNA
seurat
integrate
updated 23 hours ago by
Picasa
▴ 640 • written 3.5 years ago by
SupBioInformatics
▴ 70
1
vote
2
replies
3.8k
views
How can run cd-hit-est with a clstr threshold less than 0.8?
cd-hit
cluster
updated 9 hours ago by
Asaf
10k • written 6.3 years ago by
m.koohi.m
▴ 120
2
votes
6
replies
2.2k
views
Tool:
Python script to query GeneCards to get EntrezID, symbol from Ensembl geneID
biomart
annotation
Ensembl
updated 3 hours ago by
Mike Smith
★ 2.0k • written 2.8 years ago by
Shred
★ 1.4k
2
votes
4
replies
1.0k
views
samtools mpileup error - 1 samples in 1 input files
samtools
BAM
mpileup
SAM
updated 10 minutes ago by
Damla
• 0 • written 2.4 years ago by
joseph.kelly.94
▴ 10
2
votes
6
replies
408
views
Harmony integration group.by.var parameter
single-cell
harmony
updated 19 hours ago by
jared.andrews07
★ 17k • written 3 days ago by
Picasa
▴ 640
1
vote
7
replies
396
views
samtools write-index
samtools
15 hours ago by
R.L.
• 0
2
votes
3
replies
309
views
How do we do quantification using stringtie merge option for all the merged samples generated.
stringtie
quantification
8 hours ago by
Varsha
• 0
1
vote
2
replies
258
views
Failed to download data from EBI with ascp
EBI
aspera
updated 12 hours ago by
孝中
• 0 • written 6 weeks ago by
biock
▴ 60
0
votes
3
replies
232
views
How to add Ensembl ids after Pseudobulk analysis by DESeq2
Seurat
Pseudobulk
single-cell
DESeq2
scRNA
updated 5 hours ago by
ATpoint
82k • written 1 day ago by
Sara
▴ 30
0
votes
2
replies
212
views
perl Error - needLargeMem Bigwig
Bigwig
perl
mitosalt
7 hours ago by
marco.barr
▴ 130
0
votes
2
replies
208
views
Tools for chromosomal aneuploidy detection
genetics
aneuploidy
NGS
human
updated 9 hours ago by
a.alnawfal.1992
▴ 260 • written 4 days ago by
adarsh_pp
▴ 40
3
votes
4
replies
190
views
Invalid CIGAR after using bam clipOverlap
validatesamfile
cigar
bam
clipoverlap
11 hours ago by
MboiTui
▴ 20
0
votes
1
reply
185
views
BAM to Bedgraph creating an empty file
Bisulfite-seq
bismark
updated 6 hours ago by
raphael.B
▴ 520 • written 3 days ago by
irebekah.c
• 0
0
votes
1
reply
160
views
How to decrease the motif score?
scores
Motif
updated 10 hours ago by
ATpoint
82k • written 2 days ago by
Hadia
• 0
0
votes
1
reply
145
views
Facing problem with single cell rna seq annotation using singleR
annotation
singleR
scRNAseq
updated 19 hours ago by
jared.andrews07
★ 17k • written 1 day ago by
sc_analysis
• 0
0
votes
2
replies
97
views
Help me with Heatmap
RNA
R
seq
DESeq2
updated 1 hour ago by
MolGeek
▴ 50 • written 4 hours ago by
vmpsb
• 0
2
votes
2
replies
81
views
How do i calculate the mean of triplicates in a data.frame based on pattern?
tidyverse
r
mean
summarize
updated 4 hours ago by
dariober
14k • written 5 hours ago by
Assa Yeroslaviz
★ 1.9k
0
votes
0
replies
70
views
virus genome annotation
annotation
gff3
consensus
NCBI
coding_regions
2 hours ago by
Ghada
• 0
0
votes
1
reply
68
views
Salmon vs Kallisto vs RSEM
quantification
kallisto
Salmon
transcriptomic
RSEM
updated 2 hours ago by
Rob
6.6k • written 5 hours ago by
Mohamed Abderrahmane
▴ 20
0
votes
0
replies
67
views
Determining rs ids from SNP HGV base ID?
base
RsID
SNP
ID
HGV
17 hours ago by
Katherine
• 0
1
vote
0
replies
66
views
Search within posts based on tags using the Biostars API
api
meta
biostars
9 hours ago by
Bálint
▴ 10
0
votes
0
replies
63
views
Subset of Transcripts- How do I proceed with it?
Stringite
Quantification
9 hours ago by
Varsha
• 0
0
votes
0
replies
60
views
Imputed data doesn't match directly genotyped APOE genotype
APOE
directgenotyping
imputation
19 hours ago by
kl
▴ 10
0
votes
0
replies
51
views
PyRMD
Virtual
Screening
learning
cheminformatics
machine
11 hours ago by
s
• 0
0
votes
2
replies
33
views
identify the coordinate for coding and non_coding region.
coding
non_coding
1 hour ago by
Ghada
• 0
0
votes
0
replies
21
views
Help with proteomics downstream analysis
spectrometry
mass
proteomics
2 hours ago by
Álvaro
• 0
29 results • Page
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Recent Votes
Answer: How do i calculate the mean of triplicates in a data.frame based on pattern?
How do i calculate the mean of triplicates in a data.frame based on pattern?
C: snpEff assigned all variants as modifier intergenic
A: Problem in indexing toplevel genome with HISAT2
C: The Biostar Handbook. A bioinformatics e-book for beginners.
Answer: Error with BiocParallel. No barcodes files found
Error with BiocParallel. No barcodes files found
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Recent Replies
Comment: samtools mpileup error - 1 samples in 1 input files
by
Damla
• 0
Could you find a solution to your problem?
Comment: txt file to bigwig
by
sogand
• 0
Hi all, I am new to these kind of analysis and appreciate any guidance on my issue here: I have analyzed peakcalling .txt files that are r…
Answer: Help me with Heatmap
by
MolGeek
▴ 50
Hello! So, what is the correct design ? You will have to ask yourself, what do you want to compare? WT vs mut? If so it will be strain. 2…
Answer: Help me with simple data for RNA seq
by
swbarnes2
14k
1) you have to say what question you are actually asking. There are few different designs that would address different questions. 2) work…
Comment: identify the coordinate for coding and non_coding region.
by
Ghada
• 0
mmmm I am not sure. This is how I generate my consnsus sequence # Get consensus fastq file samtools mpileup -uf KT992094.1.fasta…
Comment: identify the coordinate for coding and non_coding region.
by
GenoMax
142k
Why do you have those N's at the beginning of the sequence? If the remainder of the sequence matches 100% then the initial N's may be wrong…
Answer: Salmon vs Kallisto vs RSEM
by
Rob
6.6k
It's nice that you've gone ahead and done some analysis of these results and their differences on your data yourself. These more general qu…
Comment: Python script to query GeneCards to get EntrezID, symbol from Ensembl geneID
by
Mike Smith
★ 2.0k
In this location there is an "entrez" file which maps ensembl IDs to Entrez. It's probably as definitive as you're going to find: https://…
Comment: Python script to query GeneCards to get EntrezID, symbol from Ensembl geneID
by
Anya
• 0
Tried it just recently with almost the same results. 456 out of 496 IDs for protein-coding genes returned as "NA" even though I can see NCB…
Answer: Download All The Bacterial Genomes From Ncbi
by
2284046470
• 0
wget https://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria/assembly_summary.txt awk -F '\t' '{if($12=="Complete Genome" && $11=…
Answer: How do i calculate the mean of triplicates in a data.frame based on pattern?
by
dariober
14k
I'm a happy user of [data.table](https://rdatatable.gitlab.io/data.table/): ``` library(data.table) dat <- structure(list(sgrna = c("Cont…
Comment: How do i calculate the mean of triplicates in a data.frame based on pattern?
by
Assa Yeroslaviz
★ 1.9k
I know it can be done with something like that: ``` cbind(p767.AM = (rowMeans(p767[,2:4])), p767.MM = (rowMeans(p767[,5:7]…
Comment: How to add Ensembl ids after Pseudobulk analysis by DESeq2
by
ATpoint
82k
Why is your `GeneName` column in mapped a mix of Ensembl IDs and gene names? What Jared wants to say is that during the preprocessing you s…
Comment: Python script to query GeneCards to get EntrezID, symbol from Ensembl geneID
by
GenoMax
142k
> only give me partial results It is possible that not every Ensembl ID is going to convert to Entrez ID. Have you tried: https://www.b…
Comment: BAM to Bedgraph creating an empty file
by
raphael.B
▴ 520
You have a space in your reference path. Not sure it's intended?
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