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113,939 results • Page
1 of 2279
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0
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3
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Need to PrepSCTfindMarker again after subset if the original object has already been normalized?
FindMarker
Seurat
3 minutes ago by
Adrian
• 0
0
votes
7
replies
65
views
How to download multiple genome files using command line (MacOS) using datasets
Bacteria
Genome
updated 12 minutes ago by
GenoMax
136k • written 1 hour ago by
scholaraspect2008
• 0
1
vote
1
reply
28
views
GEO dataset Microarray data analysis help
microarray
NCBI
GEO
R
data
just now by
Confused_human
▴ 20
773
votes
164
replies
129k
views
107 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 8 weeks ago by
Biostar
2.3k • written 7.0 years ago by
Istvan Albert
99k
0
votes
3
replies
65
views
Microarray batch correction method suggestions
microarray
log2_normalized
batch_correction
multiple_datasets
updated 44 minutes ago by
ATpoint
78k • written 3 hours ago by
Sumeet
• 0
0
votes
0
replies
42
views
GAPIT p-value significance threshold
GAPIT
p-value
GWAS
7 hours ago by
Clayton
• 0
0
votes
0
replies
49
views
Enzyme commission number in ncbi Gene database
number
commission
enzyme
7 hours ago by
Maatary
• 0
2
votes
1
reply
100
views
Best way to normalize transcript reads data for PCA & correlation and further biostat analysis
transcript_reads
updated 8 hours ago by
Jeremy
▴ 860 • written 11 hours ago by
Faith
▴ 40
2
votes
2
replies
116
views
Help with gatk CreateSequenceDictionary
GATK
updated 5 hours ago by
GenoMax
136k • written 9 hours ago by
Chris
▴ 230
2
votes
4
replies
234
views
FastQC without yellow box
fastqc
12 hours ago by
lobelino
• 0
0
votes
1
reply
95
views
Java error while running HiCDC overview code
R
Juicer
HiC
HiCDCPlus
updated 9 hours ago by
Brian Bushnell
20k • written 13 hours ago by
isMM
• 0
0
votes
0
replies
53
views
error when installing gistic2 using conda
env
gistic2
conda
13 hours ago by
luckyday1661
• 0
0
votes
0
replies
66
views
Expression differs when running plotTranscripts vs boxplot of FPKM or coverage values (R)?
R
updated 13 hours ago by
Ram
41k • written 13 hours ago by
boone5jones
• 0
0
votes
0
replies
54
views
Differing output: vcftools' --weir-fst-pop and R hierfstats package's varcomp.glob()
vcftools
hierfstats
fst
13 hours ago by
S
• 0
1
vote
2
replies
188
views
RNA-seq log2 fold change to linear
RNA-seq
DGE
updated 15 hours ago by
jared.andrews07
★ 16k • written 20 hours ago by
hmiller
• 0
74
votes
32
replies
4.8k
views
12 follow
Tool:
ChatGPT optimized for bioinformatics questions
gpt
updated 13 hours ago by
Ram
41k • written 6 months ago by
Sasha
▴ 770
0
votes
2
replies
131
views
what should I do if I get a compromised sample of scRNA-seq data?
scRNA-seq
data
snRNA-seq
updated 1 hour ago by
ATpoint
78k • written 16 hours ago by
wangjb702
• 0
1
vote
0
replies
71
views
Tool:
De Novo assembler (in C, supports MPI parallelism) available for experimenting with
de-novo
trie
olc
updated 13 hours ago by
Ram
41k • written 16 hours ago by
Graham
▴ 10
0
votes
0
replies
61
views
Comparing 16S rRNA (culture) sequences with metagenome
metagenome
shotgun
rRNA_culture
16S
updated 16 hours ago by
Ram
41k • written 16 hours ago by
aswin
• 0
0
votes
2
replies
136
views
Filling gaps in BAM file
bamtools
samtools
gene
bam
16 hours ago by
hemr3
• 0
0
votes
1
reply
115
views
Annotation GTF/GFF Arabidopsis thaliana
Arabidopsis
GFF
GTF
Annotation
11 hours ago by
enriquesan
• 0
1
vote
3
replies
182
views
vcftools
vcftools
updated 13 hours ago by
Ram
41k • written 17 hours ago by
sevda
• 0
1
vote
1
reply
103
views
Can't do runPCA after merging a splited Seurat object before UMAP
scRNA-seq
Seurat
updated 16 hours ago by
antonioggsousa
3.0k • written 18 hours ago by
wanaga3166
▴ 10
0
votes
0
replies
60
views
How do I pick the best conditions for scATAC-Seq after a series of bulk test runs?
ATAC-seq
17 hours ago by
cyril-cros
▴ 940
0
votes
1
reply
96
views
Microbial gene coverage from blast result
gene
coverage
2 hours ago by
aanchal.yadav
• 0
0
votes
0
replies
66
views
extracting Uniprot IDs for Kegg pathways
mapping
uniprot
R
kegg
clusterprofiler
19 hours ago by
Assa Yeroslaviz
★ 1.8k
0
votes
3
replies
203
views
Project Associate
GO
annotation
updated 18 hours ago by
Ram
41k • written 21 hours ago by
Pooja
• 0
2
votes
0
replies
88
views
Herald:
The Biostar Herald for Monday, December 04, 2023
herald
20 hours ago by
Biostar
2.3k
3
votes
3
replies
176
views
how to calculate duplicated reads in single cell RNA 10x genomics data
singlecellRNA
10x-genomics
updated 5 hours ago by
GenoMax
136k • written 21 hours ago by
archanaverma433
▴ 10
0
votes
1
reply
81
views
Funannotate iprscan Creates empty file
funannotate
interproscan
fungus
annotation
22 hours ago by
Umer
▴ 50
0
votes
0
replies
53
views
News:
Online course: Introduction to Python, February 12th-March 11th, 2024
python
courses
22 hours ago by
Sole
• 0
0
votes
2
replies
136
views
An issue with gtf file (ballgownrsem)
Ballgown
RNA-seq
GTF
RSEM
updated 22 hours ago by
rpolicastro
12k • written 23 hours ago by
cucindarko51
• 0
0
votes
1
reply
229
views
Issue softclipping reads when they belong and don't belong to a common amplicon
Samtools
softclip
updated 23 hours ago by
aw7
▴ 210 • written 3 days ago by
ManuelDB
▴ 80
2
votes
2
replies
142
views
4 Fastq files for a single run generated by 10X
scRNA-Seq
Fastq
SRA
10X
1 hour ago by
hkarakurt
▴ 180
0
votes
2
replies
515
views
How to resolve the error of protein lacking a stop codon when using GenomeThreader for homology prediction?
genome
threader
8 hours ago by
peanut
• 0
4
votes
6
replies
501
views
6 follow
Forum:
Bioinformatics: what do you think of it in the next 20 years?
future
updated 18 hours ago by
Ram
41k • written 3 days ago by
Daniel
• 0
0
votes
1
reply
106
views
Process Truncated fastq file
fastqc
fastq
updated 1 day ago by
GenoMax
136k • written 1 day ago by
waqaskhokhar999
▴ 150
2
votes
5
replies
213
views
kallisto index build difference according to version
index
version
kallisto
updated 22 hours ago by
dsull
★ 5.1k • written 1 day ago by
estilo
• 0
0
votes
1
reply
215
views
How to convert UNITE dataset into ecoPCR format to perform insilico PCR?
obiconvert
ecoPCR
updated 1 hour ago by
vinranke-adel0j
• 0 • written 6 weeks ago by
shristymaurya012
• 0
9
votes
9
replies
544
views
6 follow
Which language use as a beginner in Bioinformatics and Computational genomics
Computational-genomics
updated 16 hours ago by
Mensur Dlakic
★ 25k • written 2 days ago by
2021ag7698
▴ 10
1
vote
1
reply
118
views
locuszoom error
locuszoom
updated 1 day ago by
GenoMax
136k • written 1 day ago by
nanodano
▴ 30
0
votes
2
replies
196
views
sequencing data from different samples in the Integrative Genome Viewer (IGV)
IGV
VARIANT
updated 16 hours ago by
Ram
41k • written 1 day ago by
José de la Trinidad
• 0
0
votes
2
replies
505
views
Understanding gene level copy number data from TCGAbiolinks
CNV
TCGA
updated 1 day ago by
Zhenyu Zhang
★ 1.1k • written 13 months ago by
billyK
• 0
2
votes
3
replies
242
views
Error in blast+
PowerShell
blast
Windows
updated 17 hours ago by
Ram
41k • written 1 day ago by
Alexis
• 0
1
vote
3
replies
314
views
Bam files generated with STAR cause a segmentation fault core dump error when used with another tool
RNA-Seq
mapping
updated 1 day ago by
GenoMax
136k • written 1 day ago by
bkffadia
• 0
0
votes
1
reply
161
views
using RMA normalized microarray in Limma
GEOdatabase
Microarray
limma
RMA
updated 1 day ago by
ATpoint
78k • written 2 days ago by
fluke
• 0
1
vote
1
reply
177
views
Can't install hisat2 with miniconda
unix
miniconda
hisat2
updated 17 hours ago by
Ram
41k • written 2 days ago by
Ozymandeus
▴ 30
0
votes
2
replies
197
views
RNA seq
Differential-gene-expression
updated 17 hours ago by
Ram
41k • written 1 day ago by
Byonkesh
• 0
0
votes
0
replies
210
views
How to estimate -g genome-size for Flye for de novo genome or for --meta mode when using Metaflye?
assembly
fasta
genomics
nanopore
pacbio
updated 1 day ago by
shelkmike
★ 1.1k • written 4 days ago by
O.rka
▴ 710
0
votes
0
replies
107
views
Should I perform eQTL colocalization for just one of eGenes at a time?
colocalization
coloc
eCaviar
eQTL
2 days ago by
maximal_life
▴ 20
113,939 results • Page
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Recent Votes
Comment: 4 Fastq files for a single run generated by 10X
Comment: 4 Fastq files for a single run generated by 10X
Answer: How do you generate TMM normalized counts using EdgeR?
The Biostar Handbook. A bioinformatics e-book for beginners.
GEO dataset Microarray data analysis help
C: Batch effects : ComBat or removebatcheffects (limma package) ?
Answer: Batch effects : ComBat or removebatcheffects (limma package) ?
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Recent Replies
Comment: How to download multiple genome files using command line (MacOS) using datasets
by
GenoMax
136k
You can use ./datasets download genome accession --inputfile file_name_w_accession `file_name_w_accession` should contain one access…
Comment: How to download multiple genome files using command line (MacOS) using datasets
by
Michael
53k
here https://stackoverflow.com/a/1521498 is an example how to use read and for loop, you just need to put in your command.
Answer: How to download multiple genome files using command line (MacOS) using datasets
by
Michael
53k
You need to look into bash scripting regarding reading from a file and using the input in a for loop. How to combine these is explained her…
Comment: GEO dataset Microarray data analysis help
by
Basti
★ 1.9k
First I advise you to take time to correctly edit your post so that your code is readable. Secondly, you provide a lot of irrelevant code l…
Comment: How to download multiple genome files using command line (MacOS) using datasets
by
scholaraspect2008
• 0
hi there, thanks for the reply, is it possible to disclose an example of ./datasets script for that? thank you very much. i m currently try…
Comment: How to download multiple genome files using command line (MacOS) using datasets
by
Michael
53k
> you can use the commands of curl , wget and slow5curl to download the data from database. Not in this situation, it is much easier to us…
Comment: Microarray batch correction method suggestions
by
ATpoint
78k
Makes no sense in my opinion. It's different experiments that cannot be quantitatively compared.
Comment: How to download multiple genome files using command line (MacOS) using datasets
by
scholaraspect2008
• 0
by means of that, how should i write my scripting? say i have GCF000001 GCF000002 GCF000003 btw sorry if i wasn't that clear with the …
Comment: 4 Fastq files for a single run generated by 10X
by
hkarakurt
▴ 180
Thank you for your detailed answer. I will check the reads and compare them with chemistry manual as you suggested. Thank you again for yo…
Comment: Microarray batch correction method suggestions
by
Sumeet
• 0
Thank you @atpoint for your response. However, aim of analysing to generate a matrix with all dataset available after batch correction.
Comment: what should I do if I get a compromised sample of scRNA-seq data?
by
ATpoint
78k
Agreed. I would just force the cells to 5000 or so, and then proceed with the normal QC. If there's a lot of trash "cells" in the dataset t…
Comment: How to download multiple genome files using command line (MacOS) using datasets
by
rj.rezwan
• 0
you should use the `wild cards` to download all the given above GCF files. Moverover, you can use the commands of `curl` , `wget` and `slow…
Comment: Microarray batch correction method suggestions
by
ATpoint
78k
This has been asked so many times before. Analyse them separately, then make a statement on reproducibility of results using a meta-analysi…
Comment: Microbial gene coverage from blast result
by
aanchal.yadav
• 0
What is qcovhsp (high scoring segment pair) in BLAST output. Can we use this parameter to calculate the gene coverage?
Answer: Best way to normalize transcript reads data for PCA & correlation and further bi
by
Jeremy
▴ 860
Scaling the data will give you Z-scores. This is a standard way of preparing data for PCA. I would also suggest trying a center-log-ratio…
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