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Limit : this year
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1,000 results • Page
2 of 20
Sort: Votes
Rank
Views
Votes
Replies
6
votes
2
replies
839
views
Can the input file name be the same as the output file in `samtools sort`?
Samtools
updated 10 months ago by
Ram
43k • written 2.2 years ago by
Dan
▴ 180
6
votes
12
replies
2.0k
views
Help with error in cellranger
Cellranger
updated 11 months ago by
GenoMax
141k • written 11 months ago by
Chris
▴ 260
6
votes
6
replies
3.2k
views
ChIP-Seq Intensity Analysis
R
ChIP-Seq
updated 11 months ago by
Ram
43k • written 6.4 years ago by
solveforj
▴ 20
6
votes
7
replies
1.7k
views
Bioinformatics Master Project With More Focus on Developing Algorithm and Software
Masters
Algorithm
Software
updated 11 months ago by
Ram
43k • written 6.9 years ago by
nilo
▴ 90
5
votes
3
replies
1000
views
abyss-pe genome assembly
konnector
abyss-pe
updated 10 months ago by
Ram
43k • written 5.2 years ago by
Igor Lalin
• 0
5
votes
7
replies
2.7k
views
DESeq2 for differential gene expression on GTEx dataset
differential-gene-expression
RNA-Seq
GTex
DESeq2
updated 17 days ago by
Ram
43k • written 6.4 years ago by
vikram
▴ 10
5
votes
4
replies
680
views
FASTQ to BAM to CRAM to FASTQ
Samtools
5 months ago by
ManuelDB
▴ 80
5
votes
6
replies
806
views
Calculate the percentage of genomic region covered from the BED file.
NGS
sequencing
genomics
exome
genes
updated 9 months ago by
rfran010
▴ 900 • written 9 months ago by
adarsh_pp
▴ 40
5
votes
35
replies
3.6k
views
Reduce set of chromosomes in Pangenome graph
pangenome
vg
updated 9 months ago by
Jordan M Eizenga
▴ 460 • written 10 months ago by
anivlete
• 0
5
votes
7
replies
1.4k
views
error while using cyvcf2 to parse the vcf file
cyvcf2
vcf
htslib
updated 11 months ago by
Ram
43k • written 23 months ago by
rheab1230
▴ 140
5
votes
1
reply
682
views
Learning Linux advance commands
grep
awk
linux
sed
updated 6 months ago by
Zhitian Wu
▴ 60 • written 18 months ago by
rheab1230
▴ 140
5
votes
11
replies
997
views
Make heatmap for RNA-seq with non replicate
RNA-seq
updated 8 months ago by
Ram
43k • written 8 months ago by
Chris
▴ 260
5
votes
3
replies
604
views
Strand bias in supplementary alignments from Nanopore
minimap2
nanopore
strand
updated 5 months ago by
cmdcolin
★ 3.8k • written 5 months ago by
dariober
14k
5
votes
8
replies
1.9k
views
looking for tools to detect RNA contamination in DNA
RNA-Seq
DNA-Seq
contamination
QC
updated 6 months ago by
Jingjingzhang
• 0 • written 3.7 years ago by
from the mountains
▴ 230
5
votes
1
reply
617
views
Enricher with Gene Symbols
DGE
ClusterProfiler
Enrich
ORA
updated 8 months ago by
bk11
★ 2.4k • written 8 months ago by
Manuel Sokolov Ravasqueira
▴ 100
5
votes
8
replies
2.4k
views
SV calling using giraffe/vg
vg
Giraffe
calling
structural
variant
updated 9 months ago by
Jordan M Eizenga
▴ 460 • written 15 months ago by
TN
• 0
5
votes
3
replies
537
views
Visualisation of accessible regions in single cell atacseq data
visualization
scATAC-seq
single-cell
updated 7 months ago by
Ram
43k • written 7 months ago by
sarahmanderni
▴ 100
5
votes
6
replies
1.4k
views
DESeqDataSetFromHTSeqCount function taking long time and utilizing more RAM
DESeq2
R
RNA-Seq
updated 10 months ago by
Ram
43k • written 4.0 years ago by
Ranan Jyoti Sarma
▴ 90
5
votes
5
replies
628
views
Counting 705 fasta header characters ('>') in human genome
human-genome
genetics
updated 6 months ago by
ATpoint
82k • written 6 months ago by
10mz1
▴ 10
5
votes
5
replies
516
views
Example MAF Files
MAF
updated 4 months ago by
Ram
43k • written 4 months ago by
anasjamshed
▴ 120
5
votes
5
replies
643
views
Normalization and Genome-Wide Comparisons with Chipseq
chip-seq
Chipseq
Normalization
updated 4 months ago by
Ankit
▴ 500 • written 4 months ago by
zbeddingfield3
▴ 10
5
votes
5
replies
560
views
Generate BED file
bed
11 weeks ago by
daffodil
▴ 10
5
votes
1
reply
682
views
Challenges in Variant Calling and Genotyping with Short-Read Data Mapped to a Pangenome Graph: Seeking Guidance
vg
pggb
giraffe
updated 6 months ago by
Jordan M Eizenga
▴ 460 • written 6 months ago by
Kyran
▴ 30
5
votes
7
replies
939
views
Salmon index not progressing
salmon
updated 7 months ago by
Michael
54k • written 7 months ago by
camillab.
▴ 160
5
votes
7
replies
956
views
Are datasets for a unique cells, that downloded using sratoolkit?
RNA-Seq
sequencing
updated 11 months ago by
supernovamik
• 0 • written 4.3 years ago by
ee.mohseni.alert
▴ 50
5
votes
2
replies
917
views
Recommended way to normalize SmartSeq2 gene expression matrix to better match 10X expression data
rna-seq
smartseq2
r
updated 6 months ago by
yhdist
▴ 70 • written 7 months ago by
Cookin
▴ 10
5
votes
8
replies
1.9k
views
snpeff install error
snpeff
updated 11 months ago by
Ram
43k • written 12 months ago by
bestone
▴ 30
5
votes
7
replies
3.2k
views
8 follow
bwa mem -T (alignment score) not doing anything
SNP
genome
sequence
updated 6 months ago by
Istvan Albert
100k • written 5.9 years ago by
chris.bird
▴ 10
5
votes
8
replies
600
views
Multiple threads on ubuntu server
Ubuntu
updated 3 months ago by
colindaven
6.4k • written 3 months ago by
oghzzang
▴ 50
5
votes
4
replies
1.2k
views
Converting Bam file to Fasta (Zipped)
bedtools
samtools
updated 10 months ago by
Ram
43k • written 18 months ago by
Eliveri
▴ 350
5
votes
10
replies
849
views
Error when viewing a bam file
samtools
updated 10 months ago by
Ram
43k • written 12 months ago by
Chris
▴ 260
5
votes
4
replies
1.7k
views
Detection of DE genes among different tissues of an organism during time - RNA seq
detection
DE-genes
multi-treatments
time-series
updated 11 months ago by
Ram
43k • written 7.8 years ago by
statfa
▴ 760
5
votes
19
replies
4.0k
views
8 follow
Hisat2 aligner problem
RNA-Seq
ChIP-Seq
alignment
Assembly
software error
updated 4 months ago by
ATpoint
82k • written 4.9 years ago by
ta_awwad
▴ 340
5
votes
8
replies
1.0k
views
sc-RNA seq pipeline
scRNA-seq
NGS
RNA-Seq
3 months ago by
subhiksha
▴ 30
5
votes
5
replies
7.2k
views
Converting scRNA-Seq to Bulk-RNASeq
scRNASeq
bulk-RNASeq
RNA-Seq
single-cell
updated 16 days ago by
veldahan86
• 0 • written 3.8 years ago by
Assa Yeroslaviz
★ 1.8k
5
votes
8
replies
3.7k
views
Many Differentially expressed genes but few GO terms
differential-gene-expression
RNA-seq
gene-ontology
updated 17 days ago by
Ram
43k • written 6.5 years ago by
firestar
★ 1.6k
5
votes
7
replies
830
views
About the value in bigwig file
ATAC-seq
updated 9 months ago by
rfran010
▴ 900 • written 9 months ago by
Chris
▴ 260
5
votes
5
replies
2.4k
views
Quickly retrieve reference genome sequence within python
sequence
python
updated 5 months ago by
Feng Tian
▴ 20 • written 5.6 years ago by
gewa
▴ 20
5
votes
3
replies
353
views
samtools view: error reading file
samtools
bowtie2
updated 7 weeks ago by
bioinfo_ga
▴ 70 • written 7 weeks ago by
ray
• 0
5
votes
11
replies
1.3k
views
Interpret IGV output inversion
variant-calling
IGV
alignment
updated 8 months ago by
cmdcolin
★ 3.8k • written 8 months ago by
pablo
▴ 300
5
votes
2
replies
1.8k
views
Batch effects from sequencing samples accross multiple flow cells.
rna-seq
batch
batch-effect
sequencing
updated 10 days ago by
Ram
43k • written 2.9 years ago by
Mat
▴ 60
5
votes
6
replies
1.7k
views
Filter out Bam not overlapping with Bed File (keeping a read and its mate)?
samtools
bam
bed
updated 10 months ago by
Ram
43k • written 18 months ago by
Eliveri
▴ 350
5
votes
5
replies
1.8k
views
bio-newbie / gene research / tools and methods
methods
research
gene
updated 11 months ago by
Ram
43k • written 6.3 years ago by
wizofe
• 0
5
votes
6
replies
396
views
7 follow
Seeking Help with Unexpected MA Plot Output
MAplot
RNAseq
Rstudio
updated 24 days ago by
Istvan Albert
100k • written 25 days ago by
Pumla
• 0
5
votes
10
replies
1.3k
views
the distribution of log2Fc and t value are not similar for bulk RNA-seq
decoupleR
RNA-seq
8 months ago by
alwayshope
▴ 40
4
votes
11
replies
1.8k
views
PCA WITH PLINK
PLINK
updated 8 months ago by
Kevin Blighe
87k • written 8 months ago by
Michelle Guerra
• 0
4
votes
5
replies
1.4k
views
Distributed / parallel computing in bioinformatics
distributed-computing
updated 11 months ago by
Ram
43k • written 6.8 years ago by
CY
▴ 750
4
votes
3
replies
753
views
Creating custom GTF file for use with Cellranger with barcode sequences
Cellranger
7 months ago by
stefano.iantorno
▴ 70
4
votes
6
replies
955
views
Open-Source software. Good or bad for the market?
genomic-analysis
software
updated 11 months ago by
Ram
43k • written 6.2 years ago by
Bioinformatician90
• 0
4
votes
2
replies
230
views
Trying to write bwa mem -> samtools view -> samtools sort loop
bwa
samtools
mapping
genome
updated 22 days ago by
Pierre Lindenbaum
161k • written 22 days ago by
Lee
• 0
1,000 results • Page
2 of 20
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There is an Agilent array case study in the limma User's Guide, which you might find helpful and somewhat simpler. I don't recommend col…
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The comparison you've done seems exactly right to test whether treatment 2 modifies or enhances the effect of treatment 1. Have you exam…
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J
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Thank you Pierre! I'll try this out with my full data set.
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I happend to see one paper doing the similar thing, share it with you guys, "A systematic evaluation of normalization methods and probe rep…
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Please include a link when you are recommending a tool. There can be programs with similar names.
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Check out clustergrammer from Avi Ma'ayan's lab.
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